The current article believes that the intrinsic interdependence of modernity, science and secularism is an ideological non-universal interdependence but a hegemonic discourse. This kind of explanation and consideration is built upon a collection of ontological, epistemological, anthropological, methodological and evaluative sources. Based on two laws of "interchangeability of existence and science" on the one hand and "resemblance of cause and effect in the framework of causality" on the other hand, a new type of science and transcendental modernity can be contemplated. The science of religious politics and transcendental modernity but with independent epistemological foundations, sources as well as comprehensive and multi-lateral instruments in its epistemology, tries to establish a distinctive type of science for wielding and reformation in Islamic wisdom and philosophy generally and political wisdom of Islam especially in addition to two important laws of “interchangeability” and “resemblance”. However, due to stratified nature of "existence" and "science" and divine identity of existence and man  it should confess its intrinsic interdependence with the law of dependence contingency ", since it explains the existence including material, immaterial and idea etc. and human including exoteric and esoteric domains and having self and earthly as well as heavenly identities and epistemology and sources of knowledge composed of senses, experience, intellect, insight and revelation. This way it will inevitably guide to modernity and transcendental and deputation-based manipulation.