Linear Energy Transfer(LET) of heavy ion must be calculated in verification test especially for flip-chip Static Random Access Memory(SRAM)-based Field Programmable Gate Array(FPGA), in which the heavy ions must cross through several hundred micrometer of silicon substrate before reaching the sensitive volume. Single event effect mitigation of typical application on flip-chip SRAM-based FPGA is verified by using 55 MeV/μ58Ni ions accelerated by Heavy Ions Research Facility in Lanzhou(HIRFL).The LET of 58Ni ions is calculated by Stopping Range Ions Matter(SRIM)，FLUktuierendeKAskade(FLUKA) and Geometry and Tracking(GEANT) software tools and the differences are analyzed. The LET of several typical ions calculated by using SRIM also are compared with that measured by B-TOF(Magnetic Time-of-Flight) method. It is suggested that LET calculation method or software tools should be specified(especially for high energy ions)，as LET is a major Figure of Merit(FOM) of single event effect sensitivity.