Dolomite is widely present in geological history, but its origin has always been a prominent problem that troubles sedimentologists. For lacustrine dolomite, current research has not yet provided a reliable explanation for its complex genesis mechanism. The Early Cretaceous lakes in Northwest China host various morphological dolomites, providing valuable materials for exploring the origin of dolomites. According to their petrological and mineralogical characteristics, it can be divided into thick laminated dolomite, thin laminated dolomite, dolomitic mudstone, and vein dolomite. The ratios of trace elements and rare earth elements show that these dolomites precipitated in a brackish–suboxic environment. The high δ13C values (>8 ‰VPDB) of thick laminated dolomite and some thin laminated dolomite suggest the involvement of methane-producing microorganisms in the precipitation of dolomite, and the appearance of microscale/nanoscale spherical dolomite aggregates and the dispersed organic matter around dolomite particles jointly confirm that microbial-mediated biological activity promotes dolomite precipitation. The dolomite stoichiometry (mole % MgCO3) confirms that thick laminated dolomite was deposited in a restricted shallow water environment, while dolomitic mudstone is mainly deposited in relatively open water areas. The thin laminated dolomite in the shale laminae represents short-term or seasonal climatic and environmental fluctuations. In addition, some carbonate minerals of dolomitic mudstone in shallow water environment recrystallized by post-depositional hydrothermal effect, resulting in δ18O value decreased (<−10 ‰VPDB). The vein dolomite is characterized by high rare earth content and low δ13C and δ18O values, and its Sr isotope (0.712894 ± 0.000374) values reflect that the hydrothermal fluid may have been formed by the mixing of infiltrating lake water and crustal magmatic water. According to the characteristics of fluid inclusions, it is inferred that the hydrothermal fluid has the characteristics of low temperature (108.3 °C–159.8 °C), medium salinity (3.5 wt%–14.3 wt% NaCl) and high density (0.95–1.00 g/cm3). The microbial mediation and tectonic hydrothermal fluids play an important role in the formation of the Early Cretaceous lacustrine dolomite.