Hydrothermal activity is widespread in sedimentary basins, but its dual effects (chemistry and temperature) on shale reservoirs are rarely discussed. In this research, we systematically collected 33 well core samples from Q1 to Q9 units in Gulong Sag, Songliao Basin, and analyzed them using a variety of analytical techniques, including a field emission scanning electron microscopy (FE-SEM), an energy-dispersive spectrometer (EDS), X-ray diffraction (XRD), and stable C-O isotopes. Combined with the collected vitrinite reflectance (Ro), total organic carbon (TOC), and soluble hydrocarbon content data, which is the sum of free oil (pyrolysis S1) and sorb oil content (pyrolysis S2), the results show that (1) Q4 and Q8 units have large amounts of hydrothermal minerals, and its C-O isotope obviously shifts to negative, which implied those units are the main hydrothermal fluid influence area; (2) the hydrothermal activity occurred in the late depositional period of Q1–Q9 units such that its geochemistry has little effect on the proliferation of algae blooms, but its high temperature calculated by δ18O temperature formulas (around 208 °C) promoted the organic matter maturation process around Q4 and Q8; and (3) the overpressure caused by hydrothermal activity protected the shale reservoir and minimized the decrease in mineral reservoir brittleness index caused by hydrothermal fluid influence. We suggest that the shale reservoir affected by hydrothermal fluid will become a good geology “dessert”, and its upper and/or lower bounds can form an engineering “dessert” due to the precipitation of large amounts of brittle carbonate minerals.