That higher education institutions set up technology enterprise acts greatly on accelerating the transformation of scientific research achievements and complementing funds of universities, etc. But some problems which are mainly about property rights institutions of enterprise existing in the depths of the enterprise begin to appear gradually with the development of higher education institutions' technology enterprise. This paper above all discusses the logic of higher education institutions' technology enterprise arising with new institutional economics. Then it analyses why property rights institutions of higher education institutions' technology enterprise is lowly efficient. Moreover it proposes according countermeasures that are to transform the enterprise into share holding corporation. With innovation ability of general enterprise strengthens, and higher education institutions' technology enterprise and general enterprise will merge in mutual competition, and higher education institutions' technology enterprise will become product R&D center of general enterprise. This will be the developing trend of higher education institutions' technology enterprise.
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