In order to study the differential diagenesis of sandy conglomerate reservoirs in different tectonic units in eastern Junggar Basin, and establish the differential temporal sequence of burial – diagenesis – hydrocarbon charging – pore evolution, the Upper Permian Wutonggou Formation sandy conglomerate reservoir in the Dongdaohaizi Sag and Baijiahai Uplift, eastern Junggar Basin are studied, based on observation of thin sections under microscope, measurement of scanning electron microscopy (SEM), X-ray diffraction (XRD), physical properties, cathodoluminescence (CL), micro beam fluorescence, and analysis of fluid inclusions, combined with previous research results. The result shows that the reservoir displays a differential diagenetic process as they are situated at different tectonic units of the Dongdaohaizi Sag and the Baijiahai Uplift. The Dongdaohaizi Sag is dominated by continuous subsidence, the reservoir buried in relatively deep depths experienced three stages of hydrocarbon charging, which is more strongly affected by compaction, fracturing, dissolution, and late-stage cementation, the effect of middle-stage cementation is relatively weak. The pore evolution experienced four stages, including decreased porosity by shallow burial compaction, decreased porosity by moderate burial compaction and middle-stage cementation, decreased and increased porosity by moderate to deep burial middle-stage cementation and dissolution, and increased and decreased porosity by deep burial dissolution and late-stage cementation. The diagenetic stage had reached A 2 sub-stage of mesodiagenesis, and the present porosity is relatively low; however, the developed structural fractures in the reservoir has played a good role in improving the reservoir seepage capacity. By contrast, the Baijiahai Uplift is characterized by multi-stage uplift, the reservoir buried in relatively shallow depths experienced two stages of hydrocarbon charging, which is more strongly affected by middle-stage cementation, with relatively weak compaction and dissolution, fracturing, and late-stage cementation was limited. The pore evolution experienced three stages, including decreased porosity by shallow burial compaction, decreased porosity by moderate burial compaction and middle-stage cementation, and decreased and increased porosity by moderate-deep burial middle-stage cementation and dissolution. The diagenetic stage has reached A 1 sub-stage of mesodiagenesis, and the present porosity is relatively high. Two types of favorable reservoirs are developed in the study area. The first one is matrix pore favorable reservoir, which is mainly located in the area of the Baijiahai Uplift of the reservoir with relatively high porosity and permeability. The second one is structural fracture developed favorable reservoir, which is mainly located in the fault development area of the Dongdaohaizi Sag.