The aim of this article is explanation of the interdisciplinary research based on ontological assumptions in Roy Bhaskar’s view. According to the research that has been done by description- inductive method, research in Bhaskar’s view is due to transcendental argument, complexity logic, scientific explanation, methodological naturalism and explanatory critic, has interdisciplinary nature. This explanation of interdisciplinary research has an ontological base and is against epistemological approach in interdisciplinary research. According to assumptions of critical realism interdisciplinary research is in the meaning of studying a complex phenomenon at different levels of reality and explanation of its structures and external and internal mechanisms. This explanation of interdisciplinary research criticizes and reforms epistemological interdisciplinary approach. Critics involve: actualism, problem of integration and transdisciplinary. Ontological interdisciplinary research instead of actualism, focuses on explanation of structures and mechanisms that are in the real level. It considers integration as achieving knowledge based on explanation of structures and mechanisms and not as an eclectic approach and instead of transdisciplinary research focuses on keeping and interaction of disciplines. Steps of this research involve: description of an unclear phenomenon, transcendental question, redescription, resolution, integration and praxis. Principles of this research are involve investigate concrete, investigate abstract, explanatory adequacy, elimination and reform, giving alternative, education of interdisciplinary researcher , and attention to minor problems.