In order to further improve the evaluation quality of enterprise operating efficiency, reduce the error items and invalid items of partition, and improve the objectivity of operating condition evaluation, this study takes listed enterprises as an example and proposes an evaluation method of operating efficiency based on association rule algorithm and data set. In this method, the results of operating efficiency are scientifically analyzed from horizontal and vertical dimensions. The operating cost of total assets of listed companies is taken as indicators, and the correlation test is carried out by Kendall’s tau_b. From the longitudinal comparison results, it can be seen that only 12 of the 19 enterprises in the study have small-scale changes and increase year by year, accounting for 63.16%. At the same time, there are also 6 enterprises with an overall trend of decline, which objectively reflects the reasonable operation status and operation scale of enterprises in the study.