Deep fluids of the Earth are characterized by their unique physical and chemical properties, and they play important roles in various geological processes. Despite the importance of Earth’s aqueous fluids in sedimentary basins, few techniques are currently available to directly trace their origins, especially for those in the deep mantle and lower crust. In this study, we report data about fluid fillings in forms of calcites in the fractures of the Jimsar Sag, Junggar Basin, including their trace elements, Nd-C-O isotopes, Sm-Nd isochron ages and fluid inclusion features. According to comprehensive analyses of rock acoustic emission and joint rose statistics, we suggest that there are mainly three episodes of tectonic-fluid activities. As indicated by the Sm-Nd isochron ages, NW tensile fractures and NEE shear fractures in the Jimsar Sag are filled by mantle magmatism- and lower crust magmatism-related fluids at 272.4 Ma and 189.5 Ma, respectively. Subsequently, the third episode of fluid filling occurs in the NNW shear fractures at 124.3 Ma. Specifically, we emphasize that geophysical and geochemical methods should be combined to collectively constrain research on fluid activity episodes and fluid origins. Moreover, constraint on fluid activities in the deep Earth also relies on combination with regional tectonic evolution history and magmatism characteristics.