The Middle Ordovician subsalt Majiagou Formation in the Ordos Basin comprises pervasively dolomitized shallow marine limestone and is a major reservoir rich in natural gas resources. Four types of dolomite matrix and cement were identified based on petrographic textures: (very) finely crystalline, non-planar to planar-s matrix dolomite (Md1); finely to medium crystalline, planar-s to planar-e matrix dolomite (Md2); microbialites comprising dolomite microcrystals (Md3); and finely to coarsely crystalline dolomite cement (Cd). The Md1 and Md2 dolomites were controlled by alternating lagoon-shoal facies and have δ13C values (− 1.89 to + 1.45‰ VPDB for Md1, − 1.35 to + 0.42‰ VPDB for Md2) that fall within or are slightly higher than the coeval seawater, suggesting the dolomitizing fluid of evaporated seawater. Md2 dolomite was then subjected to penecontemporaneous karstification by meteoric water and burial recrystallization by sealed brines during diagenesis, as indicated by its relatively lower δ18O values (− 8.89 to − 5.73‰ VPDB) and higher 87Sr/86Sr ratios (0.708920–0.710199). Md3 dolomite comprises thrombolite and stromatolite and is interpreted to form by a combination of initial microbial mediation and later replacive dolomitization related to evaporated seawater. Cd dolomite was associated with early-formed karst system in the Md2 host dolomite. The lowest δ18O values (− 11.78 to − 10.18‰ VPDB) and 87Sr/86Sr ratios (0.708688–0.708725) and fluid inclusion data (Th: 123–175 °C) indicate involvement of hydrothermal fluid from which the Cd dolomite precipitated during deep burial. These results reveal the multi-stage dolomitization history of the Majiagou Formation and provide new constraints on fluid origins and dolomites evolution during deep burial in old superimposed basins, such as the Ordos Basin and elsewhere.