In this study, we used the side scan sonar system to investigate and evaluate the two artificial stone reef areas in A and B in the sea area of the Mayi Island in Jinzhou Bay, Dalian. The acoustic method was applied to the estimation of stone reef volume. The purpose was to explore the new estimation method of stone reef volume to improve the accuracy of the calculation results, improve work efficiency. The data mining of the sonar data was carried out by using the data processing software and the computer-aided technology. The data of the stone reef were extracted and the volume of the stone reef was estimated by the function curve. The results show that the side scan sonar image can clearly reflect the distribution of stone reefs in the seabed, and the scouring and silting degree of the stone reef can be judged according to the image. The geometric relationship and the related technical means are used to estimate the volume of the stone reef. Through several different angles of detection or with other auxiliary software errors were minimized. In the A reef area, the volume of the reef is estimated by the integral section method and the relative error is close to 16% compared with the actual volume of the reef area. The B reef area is tested and evaluated. The relative error between the evaluated volume and actual volume of the stone reff is close to 16%. The estimated volume of the two artificial fish reef areas is very different from the actual volume. Although the physical environment and the size of the reefs are different in the two reef areas, the relative error is close to and less than 20%. The integral curve is verified rationality. Therefore, under the influence of many uncertain factors, this method can estimate the volume of stone reefs relatively accurately, which can provide support and basis for the construction, management and evaluation of artificial reef area.