Reservoirs in the dolomites of the Middle Permian Qixia Formation in the Sichuan Basin are currently important oil and gas exploration objects in China. However, the questions concerning the sources of the dolomitized fluids and the control factors of the Qixia hydrothermal dolomites remain unclear. In this study, the original hydrothermal dolomites (the replacement dolomites (RDs) and saddle dolomites (SDs)) from the Qixia Formation in the southwestern Sichuan Basin (the PR1 well and Baoxing section) were mainly examined using novel in situ carbonate U-Pb dating with clumped isotopes (∆₄₇). Our results show that the U-Pb ages of the latest SDs from the PR1 well (located in the middle zone of the Emeishan large igneous province (ELIP) and distanced from the Orogenic Belt of Longmenshan) are 257.9–251.0 Ma, coincident with the period of main activity of the ELIP. Combined with the previous U-Pb dating, we propose that the high-temperature T_∆47 (82.2–108.4 °C and 127.5–205.9 °C) recorded for SDs from the PR1 well and Baoxing section may have responded to ELIP activity and Longmenshan orogeny activity, respectively. In addition, in the entire southwestern Sichuan Basin, the RDs and SDs yield similar δ¹³C and δ¹⁸O values, indicating that the dolomites were formed by hydrothermal fluids of similar sources, with marine hydrothermal fluids being a highly possible source. Finally, this study proposes a new hydrothermal dolomite genesis model for the Qixia Formation, emphasizing that the formation of hydrothermal dolomites mainly depends on the proximity to tectonic thermal events in space and time.