Sado Island in Niigata prefecture, Japan is one of the first Globally Important Agricultural Heritage Systems (GIAHS) among developed countries and has since been involved in environmental conservation agriculture (ECA). While ECA is still in its early stage in Japan, it has proven to be effective in mitigating climate change in the agricultural sector; hence, this study analyzed the factors which could contribute to the ECA continuation among Sado Island farmers. The data revealed the prevalence of farmers’ cognitive dissonance between ECA and its mitigating effects on climate change. Exploratory factor analysis and ordinal regression confirmed the importance of perceived GIAHS involvement in the continuation of ECA. In addition, other identified factors affecting ECA continuation fall either on a macro-level (i.e., farmers’ awareness of their role in improving their environment) or micro-level (i.e., farmers’ differing farm optimizations). These perspectives highlighted the altruistic nature of the Sado Island ECA farmers by valuing the improvement of their local and global environment as their main reason to continue ECA, whereas their various farm management optimizations support this observed farmer altruism by providing avenues to increase yield with only a moderate paddy land area. This study thereby highlights the need to continuously develop sustainable strategies to maintain and improve a positive farmer mindset towards ECA.