Carbonate minerals are some of the most abundant minerals on the earth. Carbonate precipitation plays an important role in many geological processes. It is a widespread phenomenon in nature that carbonate can be biologically precipitated particularly in the precipitation of calcium carbonate (CaCO3). The organisms selectively absorbed elements from surrounding environment, and assembled functional carbonate structure under strictly biological control. Moreover, the organisms induced carbonate precipitation through changing the surrounding environment. The organisms themselves could also participate in carbonate precipitation. The role and its mechanism in carbonate precipitation varied with different organisms. Here, we summarized the biological carbonate deposition and its mechanism mediated by marine plants and animals, algae organisms and bacteria organisms. The development of simulative regulation of biomineralization of CaCO3 was also discussed in this paper. Some important questions needed to be addressed in the future were proposed, and the promising application of biological precipitation of carbonate was pointed out.