The mechanism of fault-controlled hydrothermal dolomitization has long been controversial due to its complicated tectonic and diagenetic conditions, especially for the source of dolomitizing fluids and its hydrological driving models. In the southeastern Sichuan Basin, fracture-related dolomite bodies are well developed in a Middle Permian carbonate succession, providing an example of dolomitization and its relationship with regional tectonic activities. Previously, many of the dolomites in the Sichuan Basin have been interpreted as of hydrothermal origin but are usually poorly defined since it is hard to determine the nature and timing of dolomitization. In the current study, new petrographic, geochemical, and chronological data of Middle Permian dolomites have been integrated and allowed the classification of those dolomites into two categories (replacive dolomites of D1–D2 and fracture-/vug-filling dolomites of D3–D5). Calcite (C1–C3) and other non‑carbonate cements have also been found. The near-micritic dolomite (D1) was formed at the near-surface to early burial stage, likely from modified seawaters, which was reflected by its similar δ18Ofluid estimates of the parent dolomitizing fluids and rare earth element patterns to matrix lime mudstone, as well as the fabric retentive texture. The fabric destructive (D2) and fracture-/vug-filling dolomites (D3–D5) are characterized by the high estimates of δ18Ofluid of their parent dolomitizing fluids, high 87Sr/86Sr ratios, high Fe and Mn concentrations, positive Eu anomalies, high Th values, and high salinity estimates, indicating a hydrothermal origin. However, the limestone-like δ13CVPDB and strongly negative Ce anomalies of D2–D5 suggest that these dolomites may have originally evolved from seawater-derived fluids which circulated in the basal clastic rocks and flowed upwards by thermal convection through fault systems. New U–Pb ages bracketed a time range of these dolomites from 251 ± 11 Ma to 264 ± 10 Ma, coinciding with the emplacement of the Emeishan Large Igneous Province (~257–260 Ma). This may imply that the contemporary basement faulting and associated abnormal thermal event in southeastern Sichuan Basin still remotely echoed with the activities of the Emeishan Large Igneous Province, although the study area was far away from its eruption center. It facilitated the fluid circulation through fault systems and underlying sandstone aquifers and thus drove fault-controlled hydrothermal dolomitization at shallow burial backgrounds.