Methodology is one of the most important realms in every discipline such that it is regarded as the consolidation of that science. Methodology, however, cannot be separated from epistemology. Unfortunately, methodology doesn' t have gain its proper position in Islamic Economics. Most of methods used in Islamic Economics are those of conventional economics without any innovation. Explaining methodology realm, in this paper, we discuss the relation between methodology and epistemology, and between object and subject as well as the relationship among experiment, reason and value. Emphasizing Shahid Sadr and Shahid Motahari opinions, we review the method on exploring Islamic economics theories. Then, we introduce justice as a basis for methodology and epistemology in Islamic human sciences including Islamic economics. Our attempt is to propose an innovative framework for methodology based on Islamic account of Justice which is named " Haq -based Harmony".