Based on the connotation of the public perception effectiveness, this paper constructed an evaluation index system for the public perceived effectiveness of online drug purchase, including 6 first-level indicators of security, effectiveness, economy, accessibility, convenience and satisfaction, and 22 subordinate second-level indicators, and made an empirical study of the public perception effectiveness of online drug purchase by using structural equation model. The results showed that the public perception effectiveness of online drug purchase was generally close to good, and the public perceived security and effectiveness were relatively high. However, there was still a certain gap between the online drug purchase price and the public expectation, and the overall satisfaction of the online drug purchase public was not high. Based on this, it is necessary to promote medical insurance payment, improve service quality, strengthen smart supervision, enhance drug price monitoring and management and other aspects to improve the public perception effectiveness.