In order to analyze the impact of data uncertainty on the results of fish-index of biological integrity(F-IBI), a F-IBI was constructed based on the historical information and ecosystem characteristics of the surrounding waters of Chongming Island, China. A total of 12 indices related to fish species composition, trophic structure, tolerance, reproductive character, heath conditions and biomass were included in this F-IBI. Fish community information in waters near Chongming Island were collected from surveys in August and November 2020. The F-IBI was used to evaluate the state of ecosystem health of study area. Besides, the effects of survey data uncertainty on the projection of F-IBI for the surrounding waters of Chongming Island were evaluated by computer simulation. Five indices (total number of fish species, percentage of number of pollution sensitive fishes, percentage of number of piscivorous species, percentage of number of adhesive egg fishes and catch per haul per hour) from 12 indices were selected as simulation indices. The effect of single index uncertainty, multiple indices uncertainty and different levels of uncertainty on the final estimation result of F-IBI were evaluated. Results indicated that the F-IBI was in the "poor" grade of the surrounding waters of Chongming Island in August and November 2020. Uncertainty analysis showed that a set of 30% at the coefficient of variance of indices did not affect the evaluation grade of F-IBI, but the score changed to a certain extent.With the increase of index uncertainty, the fluctuation range of the evaluation results of F-IBI increased gradually. The influence strength of each index was related with the position of survey data in the range in the scoring section of F-IBI system. The results of this study emphasize the importance of considering the natural fluctuation range of the evaluation index in the evaluation of F-IBI in waters near Chongming Island.