Public opinions play an important role in the formation of Not in My Back Yard (NIMBY) conflict environmental mass events. Due to the continual interactions between affected groups and the corresponding government responses surrounding the public interests related to health, online public opinion structure reversal arises frequently in NIMBY conflict events, which pose a serious threat to social public security. To explore the underlying mechanism, this paper introduces an improved dynamic model which considers multiple heterogeneities in health concerns and social power of individuals and in government’s ability. The experimental results indicate that the proposed model can provide an accurate description of the entire process of online public opinion structure reversal in NIMBY conflict environmental mass incidents on the Internet. In particular, the proportion of the individual agents without health interest appeals will delay the online public opinion structure reversal, and the upper threshold remains within regulatory limits from 0.4 to 0.5. Unlike some previous results that show that the guiding powers of the opinion leaders varied over its ratio in a fixed-sized group, our results suggest that the impact of opinion leaders is of no significant difference for the time of structure reversal after it increased to about 6%. Furthermore, a double threshold effect of online structure reversal during the government’s response process was observed. The findings are beneficial for understanding and explaining the process of online public opinion structure reversal in NIMBY conflict environmental mass incidents, and provides theoretical and practical implications for guiding public or personal health opinions on the Internet and for a governments’ effective response to them.