In its history, there has been a strong difference between the doctrine of Sufism and the philosophical Sufism, including Indonesia. In the period of the end of the 16th century until the end of the 19th century even the emergence of the beginning of Islamic intellectualism in Indonesia was brilliantly marked by monumental works. Then, in the era of the 1970s, the discourse of renewing Islamic thought was increasingly being studied. The young generation of educated Muslims in this decade has shown a tendency towards thinking that is no longer normative in view of religion. Very different in the era of mystical and sufistic Islam. So, they tend to be more interested in Islamic understanding based on empirical and historical approaches in the formation of their religious vision. In this paper, a philosophical historical approach will be discussed on the issue of continuity and change in Islamic intellectual discourse in the Malay world of Indonesia and at the same time analyzing broader mystical and philosophical mysticism in Indonesia, friction in it, and efforts to reconcile it.