It is significant to promote the legalization process of ethnic affair governance for the legislative construction in China. This paper firstly reviews government position and value orientation in the change of ideology of ethnic affair governance from the "rule by man"to the "rule of law",then it analyses the dilemmas confronting in the legalization process: ill coordinating ethnic legal systems,deficiency of administrative intervention,conflicts between customary law and statutes and the contradictions between bureaucratic "system sluggish" and ethnic politics’ "efficiency-demand". These four factors mutually couple into complex institutional difficulties,seriously blocking the process of modernization of China’ s governance system of ethnic affairs and governance ability. This paper holds that it needs to adjust ways of thinking in ethnic legislation and break through the dilemmas in theories of legislation,perfect the mechanism of responsibility investigation,strengthen legal construction in minority areas and "de-administration" in ways of ethnic affair governance so as to promote the legalization process of ethnic affair management.