Abstract: The Mesozoic and Cenozoic strata in the Junggar basin developed two sets of shallow to semi-deep lacustrine shale, namely, the Cretaceous Qingshuihe Formation (K1q) and the Paleogene Anjihaihe Formation (E2-3a). Through organic petrology and scanning electron microscope (SEM) observation, it is found that the primary hydrocarbon-generating organic matter (OM) in the two sets of strata is different. The biological precursor of the E2-3a OM is mainly green algae (Pediastrum), while the precursor of K1q kerogen is mainly cyanobacteria (Oscillatoria). Then, the E2-3a green algae-rich shale and K1q cyanobacteria-rich shale were subjected to hydrous pyrolysis and kinetic analysis, respectively. The results show that the evolution modes of hydrocarbon generation of the typical shales are very different. Green algae have the characteristics of a low oil generation threshold, heavy oil quality, and no prominent oil peak, while cyanobacteria have the characteristics of late oil generation, concentrated hydrocarbon generation, and relatively light oil quality. The characteristics of oil generation can also be well reflected in the composition evolution of the crude oil components. The carbon isotope of gas, kerogen, and extracts of the E2-3a green algae-rich shale are significantly heavier than the K1q cyanobacteria-rich shale, which may be related to the living habits of their biological precursors, carbon source usage, photosynthesis efficiency, and carbon fixation efficiency.