The invention provides a method for preparing calcium carbonate by using catalysis of microbial carbonic anhydrase, which comprises the following steps of: adding the carbonic anhydrase extracted from a microbial culture into a liquid system containing calcium ion and bicarbonate radical ion solution or a gas diffusion system containing calcium ion solution and releasing CO2 by using ammonium hydrogen carbonate solution, performing oscillating reaction at room temperature, controlling initial pH at 5 to 10, taking out the produced sediment, and performing filtration, washing and drying to obtain the calcium carbonate. The method makes full use of microbial resources and characteristics of specificity and high efficiency of enzyme catalytic reaction, prepares the calcium carbonate by accelerated deposition, and has the advantages of riche resources, simple process, clean environment, low cost, high efficiency, quickness and the like. The calcium carbonate prepared by deposition has high purity, is calcite crystal calcium carbonate, can be used as an industrial filler, and can also be used for repairing cracks of building engineering, buildings, stone landscapes and carved stone cultural relics.