The characteristics and genesis of the calcite veins in Carboniferous basalt in the east slope of Mahu Sag, Junggar Basin are investigated based on observation of cores and thin sections; analyses of X-ray fluorescence, in situ major, trace and rare earth elements (REE), carbon, oxygen and strontium isotopes, fluid inclusions, as well as basin modeling. There are three periods of calcite fillings. The Period I calcite is characterized by low Mn content, flat REE pattern, strong negative cerium (Ce) anomaly, weak to moderate negative Eu anomaly, and light carbon isotopic composition, indicating the formation of the calcite was affected by meteoric water. The Period II calcite shows higher Mn and light REE contents, weak positive Ce anomaly and slight positive europium (Eu) anomaly, and a little heavier carbon isotopic composition and slightly lower strontium isotope ratio than the Period I calcite, suggesting that deep diagenetic fluids affected the formation of the Period II calcite to some extent. The Period III calcite is rich in iron and manganese and has REE pattern similar to that of the Period II calcite, but the cerium and europium enomalies vary significantly. The Period I and II calcites were formed in shallow diagenetic environment at approximately 250-260 Ma, corresponding to Late Hercynian orogeny at Late Permian. The Period III calcite was probably formed in the Indo-China movement during Late Triassic. It is believed that the precipitation of calcite in basalt fractures near unconformity was related to leaching and dissolution of carbonates in the overlying Lower Permian Fengcheng Formation by meteoric water, which destructed the Carboniferous weathering crust reservoirs in early stage. Relatively high quality reservoirs could be developed in positions with weak filling and strong late dissolution, such as structural high parts with Fengcheng Formation missing, distant strata from Fengcheng Formation vertically, buried hills inside lake basin, etc.