Field Programmable Gate Arrays (FPGAs) based on Static Random Access Memory (SRAM) are extremely sensitive to Single Event Upset (SEU) induced by radiation particles.In order to evaluate the dependability of the user designed FPGA circuit, a positioning fault injection methodology based on locating the configuration memory position is proposed for simulating SEU.The fault injection methodology is described from two aspects of configuration bits and user bits respectively.Fault injection tests are made on LUT and BRAM to prove the validity of the methodology.In this paper, the fault injection method, fault injection system, and fault injection tests are discussed.It is indicated that the methodology can test the key resources used in the user designed circuit with high resource coverage fraction and very low time consuming, and the methodology has good practicability.