Nowadays, the performance measurement system has been well developed. And the relations between these performance measures are playing important roles in management science. However, the effective method to analyze these relations is still underdeveloped and attracts more and more concerns. After reviewing relevant research, by adopting and further extending the essential theories of Systems Thinking, we propose a three-dimensional Systems Thinking to achieve better analysis, control and decision-making. In this paper, the rationality of the three-dimensional thought is proved first, and the modelling method is then provided in theory. Finally, a manufacturing enterprise is illustrated as an example for practical implementation.