Solving complex system challenges such as natural resource management in social-ecological systems (SESs) is fraught with great uncertainty. To cope with these challenges, socially vulnerable people in developing countries have created various autonomous innovations. This study focuses on the concept of leverage point (LP) to understand the emergence of innovations and the transformation mechanism of SESs. An LP is a part of a complex system where a small change can cause transformations in the entire system and can be identified from causal networks in an SES. This study analyzed the emergence processes of autonomous innovations as causal networks through transdisciplinary collaboration with innovators in communities and succeeded in visualizing the initial conditions, outcomes, and challenges. We constructed a new definition of LPs based on graph theory and classified LPs into three types based on their characteristics. The network analysis of the causal networks of two innovations in developing countries revealed that the three types of LPs functioned synthetically in complex systems to promote transformation. Based on these results, we propose the potential ways of interventions for the transformation of complex system networks including plural LPs and discuss their effectiveness as boundary objects in transdisciplinary processes collaborating with diverse stakeholders. Further research is expected to accumulate knowledge for solving the various challenges faced by SESs.