This paper proposes a fuzzy control scheme to achieve the high-precision and high-speed continuous transportation of ultra-thin flexible substrates with variable-section. A tension control model is presented based on the torque balance of pinches. In the model, the flexible substrate is regarded as a parallel spring-damp system, challenged by the dynamics associated with low-tension operation, besides the time-variation resulted by the variable-section. A fuzzy control algorithm is designed for the tension controller. Finally, the analysis in dynamic performance of the whole system is done using MATLAB toolbox. The simulation results show that the fuzzy control algorithm presented is effective to the tension even in transient state.