Calcium carbonate (CaCO3) precipitation is an important geochemical process. In the estuary zone and some arid shallow lakes, DOM (dissolved organic matter) and salinity are two frequent changing factors that may affect CaCO3 precipitation. The joint effect of DOM and salinity on CaCO3 precipitation kinetics and thermodynamics are still unclear. In this study, effects of DOM on CaCO3 precipitation process at 0.5‰ and 70‰ salinity were investigated by QCM (Quartz Crystal Microbalance) technique, real-time pH measurement and single-injection nanoliter ITC (isothermal titration calorimetry). The mineral crystallography was analyzed by SEM-EDS. Both DOM and salinity had inhibitory effect on CaCO3 precipitation. DOM had more pronounced inhibitory effect on CaCO3 precipitation at lower salinity. Regardless of DOM, 70‰ salinity inhibited CaCO3 precipitation >0.5‰ salinity. The CaCO3 precipitation kinetics followed the first-order kinetic model and the adhesion kinetics of the instantaneous nucleation and crystal growth stage could be well described by the exponential function. CaCO3 precipitation was an endothermic process and high salinity strongly hindered CaCO3 precipitation. The effect of DOM on the absorbed heat was significant at 0.5‰ salinity. At 70‰ salinity, regardless of the effect of DOM, CaCO3 precipitation rate was greatly slowed down because it needed much more heat. CaCO3 minerals were dominated by rhombohedral calcite while CaCO3 minerals were mainly shaped as spherical vaterite at 0.5‰ salinity and rhombohedral calcite at 70‰ salinity. The crystal phase changed during CaCO3 precipitation at 0.5‰ salinity. In conclusion, the presence of DOM had substantial impact on the micrograph of the CaCO3 minerals. The percentage of flawed crystals with rough surface increased significantly with increased DOM concentration.