Abstract: We introduced the application of FiSAT II software in the specific process of using iteration method to estimate fishing death coefficient, and compared the results from traditional Length based Cohort Analysis (LCA) with the data from FiSAT II software supported LCA. It is not difficult to find that N_F/N_T ratio of the two methods increases with increasing body length, while the difference between the two methods for intermediate group of the body length is smaller. The Virtual Population Analysis module of FiSAT II software is a good method for extrapolating to fishing mortality coefficient (F). In this method, theoretically, precision is improved by using iteration, thus the estimation of fish stock becomes more accurate. Self-control group of body length deletion experiments show that in the use of LCA for fish stock estimation, the loss of minimum body length group data causes the maximum deviation, reaching more than 10%.