Hardware transient fault is one of the top challenges for the space computers, which run in the space environment with different radiation phenomena. Furthermore, with the continuously increasing performance enabled by the scaling of VLSI technologies, modern microprocessors are becoming more susceptible to transient faults. For the reliability of system, a major effect incurred by these transient faults is the control flow errors, e.g. modifying the target address of a jump instruction. Through the control flow graph of program, basic blocks are firstly categorized by the graph coloring algorithm. Then an effective control flow checking method, named ECCFS, is presented based on the formatted signature of basic blocks. Moreover, the extended solutions are proposed for the control flow checking of intra-block and inter-procedure, respectively. ECCFS can be extended flexibly by user through configuring the signatures format according to the requirement of detecting rate and performance. The analytical result of checking capacity and the experimental result of fault injection indicate that ECCFS can detect most control flow errors, excepting the dummy branch and some checking defects. Compared with two typical control flow checking methods, ECCFS has the advantage in errors detecting rate and performance overhead.