Early Jurassic mixed siliciclastic-carbonate Mafraq Formation is the base of Sahtan Group distributed in the north part of Oman, thinly in the platform high and missing in south of Oman. The Upper Mafraq considered as reservoir in central and eastern Interior Oman. This study provides a detailed description of depositional environments and diagenetic alteration and hence of their effects on reservoir quality in two outcrops of Mafraq Formation at Wadi Muayden and Wadi Al-Sahtan of northern and southern flanks of Al-Hajar Mountain in Oman. Mafraq Formation of Wadi Muayden and Wadi Al-Sahtan outcrops was fully described and detailed description sedimentological logs were constructed. Petrography analysis has been carried out on 110 thin sections of mixed siliciclasticcarbonate samples incorporated with XRD, SEM, CL and isotopes analysis in order to evaluate the petrographic description, textural and mineral composition and diagenetic alterations. Moreover, the depositional environments of the studied Mafraq Formation have been grouped into four facies associations, which are fluvial (FA 1), coastal complex (FA 2), lagoon-backshoal (FA 3) and shoal (FA 4). Based on textural analysis, sandstone samples of Mafraq Formation in Wadi Muayden have an average of very fine-grained and moderately well sorted sandstones. Furthermore, Mafraq Formation in Wadi Al-Sahtan composed of fine-grained and moderately well sorted sandstones. The variation of grain size in sandstones is reduced toward Wadi Muayden outcrop and the shape of grains become more rounded due to the long distance of clast transportation away from the source area. Modal composition shows that Mafraq Formation composition is dominated by intrabasinal carbonate grains (echinoderms, bivalves, gastropods, brachiopods and foraminifers) and extrabasinal non-carbonate grains (quartz). Petrographic and geochemical analysis of sandstone and carbonate of Mafraq Formation have shown that these sediment has undergone varies diagenetic regimes including quartz overgrowth, compaction, dissolution and cementation by calcite, dolomite, iron oxide, anhydrite and pyrite during eo, meso- and telodiagenesis. However, during eodiagenesis, mechanical compaction exists in fluvial facies association (FA 1) effected on quartz grains. Add to that, anhydrite coated some quartz grains and filling some pores in fluvial facies association (FA 1) by providing the needed SO4 from the sea water, possibly during sea level rise and depositional of overlaying marine carbonates. It could also occurs at eodiagenesis evidenced by the absence of quartz overgrowth and/or telodiagenesis filling pores that created by dissolution. Moreover, calcite cement exists in fluvial facies association (FA 1) by the effect of humid condition. It is more dominant in coastal complex (FA 2), lagoon (FA 3) and shoal (FA 4) facies associations than fluvial facies association (FA 1) and this attributed to the presence of bioclasts. Dolomite is another type of carbonate cements that may have occurred in eo- and mesodiagenesis which was mostly form by alteration of calcium carbonate and the seawater and/or meteoric water (under semi-arid condition) providing the need of Mg2+. Although, dissolution of different bioclasts and cement is a major attribute for creating secondary porosity, but this is filled by calcite and dolomite cement at later stage. Iron oxide occurs at early and later stage of diagenesis in an oxic environment. Moreover, pyrite exists in sandstone and carbonate sediment within anoxic environment conditions as a result of eogenetic microbial activity by getting the required (SO4)2- from the seawater and filling pores during the telodiagenesis. Quartz overgrowth is more dominant in fluvial facies association (FA 1) and more common toward Wadi Al-Sahtan outcrop, affected by silica that released from the chemical compaction of quartz grains. Siderite is a diagenetic process postdating quartz overgrowth and can be caused at meso- or telodiagenesis stages. Detailed petrographic analyses showed that more facies association affected by diagenetic process at meteoric, marine and burial stages that plays an important role in decreasing of reservoir quality.