This paper aims to comprehend the essential principles of tolerance by studying the introduction of the Roman Catholic Church to Korea in the late period of Joseon Dynasty. It suggests the multidisciplinary perspective embracing historic, religious and philosophical approaches in that, in a way of a political philosophy, it analyzes the process of persecution and establishment of the Catholic Church, which reveals extremely vehement conflict between religion and politics and ensuing settlement of that religion. Especially from Baruch Spinoza's political philosophy, this study derives the theoretically crucial notion that tolerance toward religions and thoughts is highly valuable for maintenance of one governmental system, and so discusses the ways to accomplish the well-balanced condition of a society. Acknowledging Spinoza's idea that it is possible for one political power to be able to interfere in the external level of faith but never possible to control the internal principle of religious belief itself, this research firstly debates the process of acceptance of the Catholic Church and relevant historical issues in late Joseon Dynasty, attempts to clearly define the relation between religion and politics, and lastly, through the principle of tolerance, tries to find meaningful ways to manage one society in balance.