Based upon theory of ultimate ownership structure and principal-agent theory, this article raises the problems of endogeny, which is very likely to exist between ultimate ownership structure, severity of agency problems and firm performance. So the author collected panel data of 118 agricultural listed firms during 2004-2010, and constructed three-stage least square model to analyze the complicate relationships between these variables mentioned above. There were some interesting findings as following: firstly, both severities of two types of agency problems played striking negative role in ultimate ownership structure, and ultimate ownership structure was very remarkable negative to the severity of second type agency problem. Next, outcomes of the empirical analysis certified that firm performance had a great influence on the gravity of agency problems, while it could not draw a safe conclusion that two kinds of agency problems’ seriousness had impact on performance of firms. At last, ultimate ownership structure had great positive impact on firm’s performance, which, however, played a distinct negative role in ultimate ownership structure.