The Carboniferous strata in the northeastern Junggar Basin are an important exploration field for natural gas in the basin. However, volcanic rocks have long been the primary exploration target. In contrast, the exploration and research of clastic rocks associated with source formations have been largely overlooked, resulting in an insufficient understanding of the reservoir forming conditions and exploration potential of Carboniferous clastic rocks. Through the evaluation of Carboniferous source rocks, effective source stove characterization, clastic reservoir evaluation, oil and gas source correlation, and reservoir formation model construction in this region, three key findings have been made. First, the Carboniferous in the northeastern Junggar Basin has developed three sets of high-quality gas source rocks: the Dishuiquan Formation, the Songkalsu B Member, and the Shiqiantan Formation. These formations correspond to three hydrocarbon source centers: the Sannan–Dishuiquan Sag, the Wucaiwan Sag–Dajing area, and the Dongdao Haizi Sag–Baijiahai High. Second, the Carboniferous system in the northeast has developed multiple types of large-scale reservoirs, including sand conglomerates, sandstones, turbidites, dolomitic rocks, and shale. These reservoirs are generally characterized by low porosity to ultra-low porosity and low permeability to ultra-low permeability reservoirs. There is a dissolution pore development zone at depths of 2900–4500 m. Third, a comparison of oil and gas sources reveals that all three sets of gas source rocks contribute to the natural gas found in the northeast, with obvious characteristics of near-source reservoir formation. The Carboniferous clastic rocks host two types of natural gas reservoirs: unconventional and conventional near-source reservoirs. It is predicted that there is an orderly accumulation pattern of shale gas, tight sandstone gas, and conventional natural gas reservoirs. This study reveals that the Carboniferous clastic rock source and reservoir configuration in the northeastern Junggar Basin is highly favorable, and the natural gas reservoirs in source and near-source clastic rocks represent important exploration directions.