Based on the analysis of the deformation styles in different tectonic belts of the Middle-Upper Yangtze region, as well as the dissection of typical hydrocarbon reservoirs, this study determined the controlling effects of deformations on the hydrocarbon accumulations, obtaining the following results. The Middle-Upper Yangtze region experienced significant deformations during the Late Indosinian (T2–T3), the Middle Yanshanian (J3–K,), and the Himalayan, and five styles of tectonic deformations mainly occurred, namely superimposed deep burial, uplift, compressional thrusting, multi-layer decollement, and secondary deep burial. The distribution of hydrocarbon reservoirs in the piedmont thrust belts is controlled by the concealed structures on the footwall of the deep nappe. The gentle deformation area in central Sichuan experienced differential uplift, structural-lithologic hydrocarbon reservoirs were formed over a wide area. The eastern Sichuan-western Hunan and Hubei deformation area experienced Jura Mountains-type multi-layer detachment, compressional thrusting, and uplift. In relatively weakly folded and uplifted areas, conventional structural-lithologic hydrocarbon reservoirs have undergone adjustment and re-accumulation, and the shale gas resources are well preserved. In the strongly deformed areas, conventional hydrocarbon reservoirs were destroyed, while unconventional hydrocarbon reservoirs have been partially preserved. The marine strata in the Jianghan Basin experienced compression, thrusting, and denudation in the early stage and secondary deep burial in the late stage. Consequently, the unconventional gas resources have been partially preserved in these strata. Secondary hydrocarbon generation become favorable for conventional hydrocarbon accumulations in the marine strata.