Epigenetic dissolution is one of the important factors in the formation of carbonate reservoirs. In order to study the role of microorganisms in the dissolution process of carbonate rocks, three typical microorganisms, Bacillus Q1, Streptomyces Q2 and Aspergillus Q3, were screened from rock surface. The universality of carbonate rocks dissolution by microorganisms was studied by comparing acid production, dissolution rate and dynamic simulation experiments of dissolution in porous media.The results showed that the pH and Ca²⁺ concentration changed regularly in each experimental system, and the abilities of acid-producing and dissolution of Aspergillus Q3 are the most remarkable. Within five days, the pH of the Q3 culture system was reduced by 2.69, and the concentration of Ca²⁺ in Q3-calcite and Q3-dolomite culture systems reached 327 and 258 mg/L, respectively. Microbial dissolution experiments on dolomite in porous media show that the ability of Aspergillus Q3 to dissolve core is also stronger than that of Bacillus Q1 and Streptomyces Q2. Microorganisms can not only dissolve rock surface, but also dissolve carbonate rock in porous media. Microbial dissolution of carbonate rocks is universal. Microbial karst is likely to occur in a wider range of surface rocks, which is one of the important factors for the formation of carbonate reservoirs.