Understanding transcendental philosophy as a systematic system of ontology and dominance over its studied fields require paying attention to the foundations and type of methodology governing it. Transcendental philosophy is an Islamic philosophy in which there are intuition, religious text and theoretical mysticism, and knowing its methodology seems more necessary. This paper aims at solving the ambiguities and answering the questions that the researcher of Islamic philosophy, especially in transcendental philosophy, faces and considers them in conflict with the philosophical identity of transcendental philosophy. The source of these ambiguities and questions are thoughts based on the intuition of the philosopher himself or the intuition of the mystics or the religious text. In this study, after analyzing and evaluating two explanations of the methodology of transcendental philosophy, i.e. the claim of ‘context of discovery and judgment’ and the claim of ‘individual method and universal method’, we presented an explanation that can make these assertions compatible and answer the researcher’s questions in transcendental philosophy and its methodology.