Sustainability transformation as a powerful concept has become “hot spot”. Although recent studies on sustainability transformation are mostly based on resilience theory and/or transition theory theoretically and empirically, its conceptual grounds, theoretical development and practical relevance are still in infancy. In this explorative theoretical paper, based on the premise of ensuring consistency between ontology, methodology and practice, I try to face these challenges to synthesize and integrate ecological resilience theory, transition theory, realist social theory, and social-ecological theory to develop and build theory on sustainability transformation in SES to uncover specific conditions, mechanisms and patterns underlying sustainability transformation. My first step to explore this theory is to re-develop and re-conceptualize resilience thinking theory (resilience as adaptability, as transformability, and as persistence) so as to liberate resilience thinking theory from “capacity” to “dynamic process”, from “passive and negative regime shift” to “positive and active regime shift”, from “non agents of agency” to “agents of agency”. I propose Social-Ecological Transitional Resilience Thinking Framework, that is, resilience as adaptation, as transformation and as transition. The second attempt is to integrate this framework with the morphogenetic approach to constructMorphogenetic Social-Ecological System Framework (MSES)with the purpose of furnishing a theoretical framework for transformative change and process onto SES.