Despite shales have undergone complex diagenetic transformation during deep burial and thus can significantly affect the development potential of shale oil and gas reservoirs, the understanding of the diagenetic processes is still relatively poor. The main issues that need to be clarified contain the types of diagenetic minerals in shales, diagenetic evolution together with its impact factors, and the extent of element mobility behavior in such low porosity and permeability pore system, which restricts further understanding of shale reservoirs. Two black rock series of the Lower Cambrian Yurtus Formation in the northwestern Tarim Basin are utilized to examine authigenic mineral distribution and diagenetic evolution characteristics, on the basis of determination of sedimentary environment, mineral composition, clay mineral assemblage, organic carbon content and organic matter maturity. During the diagenetic evolution stage, the temporal and spatial distribution of diagenetic changes and their influencing factors are thus described. This study shows that the two black rock series are developed and controlled by two relatively complete transgressive-regressive sedimentary cycles in the shallow shelf environment, and the dominant diagenetic regime is interpreted to correspond to eodiagenesis and mesodiagenesis. Significant differences in the combination, distribution, and formation sequence of diagenetic minerals such as quartz, barite, carbonates and clay minerals occur in the two sets of black rock series, showing different diagenetic evolution affected by the sedimentary environment and hydrothermal effect. The extensive distribution of diagenetic products in the mesodiagenesis further verify a certain degree of element fluxes can be sourced both internally and externally in low porosity and permeability black shales. This study provides an important basis for further understanding the diagenetic mechanism of the Lower Cambrian black series and analyzing the development characteristics of shale reservoirs in the northwestern margin of Tarim Basin.