Soft error is a key challenge in computer systems. Without soft error mitigation, control flow error (CFE) can lead to system crash. Signature-based CFE monitoring scheme is a representative technique for detecting CFEs during runtime. However, most of the signature-based CFE monitoring schemes proposed thus far are based on a single thread. Currently, the widely used multi-threaded and multi-core environments have greatly improved the performance of the computing system, but, if the these schemes are applied in these environments, performance improvement is difficult to achieve, or rather performance degradation may occur. In this paper, we propose a separate signature-based CFE monitoring (SSCFM) scheme that separates the signature update and the signature verification on the thread level. The signature update is combined with application thread and signature verification and executed on separate monitor threads, so that we can expect performance improvements in multi-threaded or multi-core environments. Furthermore, the SSCFM scheme can fully cover inter-procedural CFE not covered by many signature-based CFE monitoring schemes by using inter-procedural control flow analysis. With the proposed SSCFM scheme, the execution time overhead is reduced by approximately 26.67% on average from the SEDSR scheme, and the average CFE detection rate with SSCFM is approximately 93.69%. In addition, this paper also introduces the LLVM compiler-based SSCFM generator that makes it easy to apply the SSCFM scheme to software applications.