Deep coalbed methane (CBM) resources are abundant in China, and in the last few years, the country’s search for and extraction of CBM have intensified, progressively moving from shallow to deep strata and from high-rank coal to medium- and low-rank coal. On the other hand, little is known about the gas content features of deep coal reservoirs in the eastern Junggar Basin, especially with regard to the gas content and the factors that affect it. Based on data from CBM drilling, logging, and seismic surveys, this study focuses on the gas content of Baijiahai Uplift’s primary Jurassic coal seams through experiments on the microscopic components of coal, industrial analysis, isothermal adsorption, low-temperature CO2, low-temperature N2, and high-pressure mercury injection. A systematic investigation of the controlling factors, including the depth, thickness, and quality of the coal seam and pore structure; tectonics; and lithology and thickness of the roof, was conducted. The results indicate that the Xishanyao Formation in the Baijiahai Uplift usually has a larger gas content than that in the Badaowan Formation, with the Xishanyao Formation showing that free gas and adsorbed gas coexist, while the Badaowan Formation primarily consists of adsorbed gas. The coal seams in the Baijiahai Uplift are generally deep and thick, and the coal samples from the Xishanyao and Badawan formations have a high vitrinite content, which contributes to their strong gas generation capacity. Additionally, low moisture and ash contents enhance the adsorption capacity of the coal seams, facilitating the storage of CBM. The pore-specific surface area of the coal samples is primarily provided by micropores, which is beneficial for CBM adsorption. Furthermore, a fault connecting the Carboniferous and Permian systems (C-P) developed in the northeastern part of the Baijiahai Uplift allows gas to migrate into the Xishanyao and Badaowan formations, resulting in a higher gas content in the coal seams. The roof lithology is predominantly mudstone with significant thickness, effectively reducing the dissipation of coalbed methane and promoting its accumulation.