Along with the growth of tourism, the eco-environments of an increasing number of tourist destinations have been threatened by natural disasters and changing traditional cultures. To investigate eco-environmental issues, some studies have focused on tourism stakeholders' pro-environmental behaviors. These studies have provided insights into pro-environmental behaviors; however, few studies have investigated the impact of natural disasters on residents' pro-environmental behaviors in tourist destinations. Some comparative analyses on the effect of culture on people's pro-environmental behaviors between different countries have been reported; however, only a few comparative analyses looking into different cultural groups within a single country have been carried out. To address these issues, we examine the relationship between culture, natural disasters and residents' behaviors toward eco-environmental conservation in two tourist destinations in Sichuan province. We collected data from the Jiuzhaigou National Park (JNP) and the Mount Qingcheng and Dujiangyan Irrigation System (MQDIS, a UNESCO World Heritage site). A total of 750 questionnaires (350 at JNP, 400 at MQDIS) were distributed; 688 were returned and 642 valid questionnaires were used for data analysis. After exploratory factor analysis, multi-group confirmatory factor analysis, and multi-group structural equation model analysis, we found the following: (1) Seven factors (altruistic values, cognition of the relationship between humans and nature, non-anthropocentrism, eco-catastrophe and natural ability, daily pro-environmental habits, eco-environmental concern in tourist destinations and awareness of natural disaster consequences) were extracted through exploratory factor analysis, and two observed variables and one factor were deleted through multi-group confirmatory factor analysis. In the end, 24 items and 8 latent variables (including 2 high-order factors: eco-environmental beliefs and behaviors toward eco-environmental conservation in tourist destinations) were certified. (2) Maintaining cultural heritage or being aware of the consequences of disasters positively affects residents' behaviors toward eco-environmental conservation in tourist destinations. The goodness-of-fit of the multi-group structural model is satisfactory for both JNP and MQDIS data. (3) Because of culture similarity between the two regional groups, JNP and MQDIS adhere to the same structure model. Furthermore, the following causal chain, altruistic values → eco-environmental beliefs → residents' behaviors toward environmental conservation in tourist destinations, strongly impacts the predictions of pro-environmental behaviors compared with other causal chains in both structure model of JNP and structure model of MQDIS. In addition, there were no significant differences in residents' altruistic values, eco-environmental beliefs and environmental-conservation behaviors between the two cultural groups. (4) Because of cultural and environmental differences, residents' personal norms, awareness of natural disaster's consequences and daily pro-environmental behaviors significantly varied; and all the corresponding standardized path coefficients in the structure model of JNP were higher than those of MQDIS. These results are important for tourism management authorities to implement effective environmental management policies, which ensure that local traditional culture thrives. Authorities also have to promote environment and disaster education to strengthen personal obligations to protect the environment. Further research is necessary to validate our model in other tourist destinations with different cultural community residents. We will also investigate the relationship between egoistic values and residents' pro-environmental behaviors in tourism destinations.