The widespread Capitanian (late Guadalupian) marine anoxia/euxinia has long been regarded as a key driver of the end-Guadalupian (middle Permian) biotic crisis. However, the cause of this marine anoxia is debated, particularly regarding the influence of the Emeishan large igneous province (ELIP). To investigate the contribution of the ELIP to marine anoxia and the possible causal mechanisms, we undertook a conodont biostratigraphic and geochemical study of the middle Permian Maokou Formation in a platform-to-trough transect in the Upper Yangtze region, South China. Our results show that the depositional facies of the Maokou Formation changed from a carbonate ramp to an intra-platform trough within the Jinogondolella (J.) altudaensis zone in the northwestern Yangtze region, which can be attributed to the initial activity of the ELIP. Mantle-derived Sr inputs in the initial and main stages of the ELIP led to two decreases in 87Sr/86Sr during the Capitanian, in the J. shannoni–J. altudaensis and J. prexuanhanensis–J. xuanhanensis zones. The elevated 87Sr/86Sr values during the late Capitanian may have been due to enhanced continental weathering caused by rapid climate warming in response to subaerial eruptions of the ELIP. The deep-water anoxia–euxinia expanded during the middle Capitanian, as indicated by increased MoEF/UEF and V/(V + Ni) values, along with the disappearance of burrows and appearance of small pyrite framboids in the J. altudaensis zone in the Cheng 20 well. However, shallow-water anoxia occurred during the late Capitanian (i.e., J. prexuanhanensis–J. xuanhanensis zone), as evidenced by positive Ce anomalies and losses of aerobic benthic species in the Erya section. Importantly, marine anoxia and negative δ13Ccarb excursions occurred synchronously, but earlier in deep water than in shallow water, potentially indicating an expansion of the oxygen minimum zone (OMZ). The deep-water anoxia corresponded to a decrease in 87Sr/86Sr ratios and the appearance of an intra-platform trough in the J. altudaensis zone, whereas the shallow-water anoxia in the late Capitanian coincided with elevated 87Sr/86Sr ratios. This suggests that the initial activity of the ELIP promoted the development of the OMZ in deep waters during the middle Capitanian, while the subaerial eruptions of the ELIP drove climate warming that led to the expansion of the OMZ into shallow-water platforms during the late Capitanian.