To establish a new quantitative analysis method for amorphous silica content and understand its effect on reservoir properties, the amorphous silica (SiO2) in the shale strata of the Lucaogou Formation in the Jimsar Depression was studied by scanning electron microscopy (SEM) observation, X-ray diffraction (XRD), and X-ray fluorescence spectrometry (XRF). Amorphous silica shows no specific morphology, sometimes exhibits the spherical or ellipsoid shapes, and usually disorderly mounds among other mineral grains. A new quantitative analysis method for observing amorphous SiO2 was established by combining XRD and XRF. On this basis, while the higher content of amorphous SiO2 lowers the porosity of the reservoir, the permeability shows no obvious changes. The higher the content of amorphous SiO2, the lower the compressive strength and Young’s modulus and the lower the oil saturation. Thus, amorphous SiO2 can reduce the physical properties of reservoir rocks and increase the reservoir plasticity, which is not only conducive to the enrichment of shale oil but also increases the difficulty of fracturing in later reservoir development.