Any new method for controlling a nonlinear system has widely been reported. An inverted pendulum system has typically been used as a target system for demonstrating its usefulness. In this paper, we propose an algorithm to control a flexible joint cart based inverted pendulum system. Two carts are connected with a spring and one is a driving cart and the other is no driving cart with a pole. We here present a system modeling and a good fuzzy logic based control algorithm. We also introduce LQR (Linar Quadratic Regulator) technique for reducing the number of control variables. By using this technique, the number of input variables for a fuzzy logic controller is become only two not six. So the computational complexity is largely reduced. Moreover, a two-input fuzzy logic controller has a control rule table with a skew-symmetric property. And it will lead the design of a single-input fuzzy logic controller. In order to demonstrate the usefulness of the proposed method and prove the superiority of the proposed method, some computer simulations are presented.