Secondary pores and carbonate cements are quite well developed in sandstones near the unconformity between Jurassic and Cretaceous strata of Yongjin area in central Junggar Basin. Data obtained by thin-sections analysis, cathodoluminescence emission analysis and SEM/EDX show that carbonate cements seem to be the uppermost cements composed of ferroan sparry calcite and ankerite and are distributed mostly in the depth interval of 100 m below the unconformity, with their contents increasing with the depth. Carbon and oxygen isotope and elements determination in mudstone values indicate that atmospheric fresh water did not have a distinct effect on reservoir characters below the unconformity, but the development of carbonate cements and pores was closely related to the organic acid. With the action of the organic acid, early carbonates, feldspar and clay minerals provided materials for later carbonates, and the dissolved matters moved to the unconformity by acidic fluids and deposited again, which led to the superimposition of high contents of porosity and carbonate cements at the depth. As the ferroan sparry carbonate cements were formed later and the sandstone reservoir was on the whole not subjected to any other constructive diagenesis, the development of carbonate cements must have played an apparent controlling effect on reservoir characteristics.