Based on 2688 groups of data during 2012-2014 of A-share market of Shenzhen and Shanghai Composite as the study sample, this article explores the influence of institutional investor on enterprise financial value and market value under the property differences. The study result shows that: The shareholding ratio of institutional investor and enterprise financial value are positively correlated; the shareholding ratio of institutional investor and enterprise market value are also positively correlated. Furthermore, this article, based on property right factors, explores the functional mechanism of the shareholding of institutional investors, finding that: Value of shareholding of institutional investors and market value in private enterprises are improved more than in SOE, indicating that governmental factors aggravate the subject of agency in SOE, and weaken the role of shareholding of institutional investors in improving the value of SOE.