Dolostone, especially replacement dolostone, is a significant component of Earth's carbonate rock archive. Hydrothermal dolostones, often associated with fault zones, play a crucial role in the dolostone record. However, the origin—particularly the sources of magnesium involved in their formation—remains unclear. This study focuses on two case examples of upper Ediacaran hydrothermal dolomite from the Yangtze Block, utilising a multi-proxy approach that examines δ26Mg, δ44/40Ca, 87Sr/86Sr ratios, and elemental concentrations. In the first study site (i.e., the central Sichuan Basin in the upper Yangtze Block), saddle dolomites of Ediacaran dolostones were measured to have fluid inclusion homogenization temperatures up to 260 °C, which are significantly higher than those the strata experienced, and are characterised by low δ26Mg values (−2.23‰ ± 0.18‰) and δ44/40Ca values (0.81‰ and 1.10‰), along with high strontium (Sr) contents (103.9 ± 56.0 ppm) and 87Sr/86Sr ratios (0.7119 ± 0.0017). These geochemical data indicate that hydrothermal dolomites were precipitated from hydrothermal fluids after obtaining Mg from chlorite-bearing crustal lithologies. Hydrothermal dolomitisation likely occurred in the mixing of crust-derived fluids and burial brines. In contrast, at the second study site (i.e., Nanshanping outcrop at the middle Yangtze Block), the presence of 26Mg-enriched (δ26Mg: −0.6‰ to −0.5‰) saddle dolomite with low Sr contents (47.0 ± 9.6 ppm) suggests the influence of mantle-derived fluids. The hydrogeochemistry of the parent fluid appears to be the primary factor controlling the δ26Mg and δ44/40Ca values, as well as the 87Sr/86Sr ratios of hydrothermal dolomite. This is further verified by hydrothermal dolomite from the Ediacaran to the Phanerozoic and diagenetic models. Low δ26Mg values combined with high 87Sr/86Sr ratios in hydrothermal dolomite generally indicate the presence of crustal fluids. Conversely, high δ26Mg values, along with low 87Sr/86Sr ratios, are typically associated with the involvement of the mantle-derived fluids. The study presents two distinct sources of Mg, typically for the formation of hydrothermal dolostones, providing some clues to solve the puzzle for the origin of dolomite, particularly in settings characterised by widespread hydrothermal fluid activity.