There are some problems in the operation of the university-running authority of universities jointly run by the mainland, Hong Kong and Macao, such as loose legislative guarantee system, poor administrative service mechanism, single dispute resolution and so on, which restricts the in-depth cooperation of higher education between the mainland and Hong Kong and Macao. According to the operation theory of law, the way of guarantee can be constructed from the dimensions of legislation, administration and legal relief. First, improve the legislative guarantee system by improving the comprehensive authorization legislative system, formulating special legislative documents and promoting the normalization planning of cross-border cooperative schools. Secondly, improve the administrative management mechanism by strengthening administrative support and establishing departmental coordination mechanism. Finally, we will comprehensively apply the educational appeal, reconsideration and litigation systems to improve the legal relief mechanism.