SRAM-based FPGAs are very susceptible to radiation-induced Single-Event Upsets (SEUs) in space applications. The failure mechanism in FPGA's configuration memory differs from those in traditional memory device. As a result, there is a growing demand for methodologies which could quantitatively evaluate the impact of this effect. Fault injection appears to meet such requirement. In this paper, we propose a new methodology to analyze the soft errors in SRAM-based FPGAs. This method is based on in depth understanding of the device architecture and failure mechanisms induced by configuration upsets. The developed programs read in the placed and routed netlist, search for critical logic nodes and paths that may destroy the circuit topological structure, and then query a database storing the decoded relationship of the configurable resources and corresponding control bit to get the sensitive bits. Accelerator irradiation test and fault injection experiments were carried out to validate this approach.