The evolution of genome editing technology based on CRISPR (clustered regularly interspaced short palindromic repeats) system, has led to a paradigm shift in biological research. CRISPR/Cas9-guide RNA complexes, enable rapid and efficient genome editing in mammalian cells. This system induces double-stranded DNA breaks (DSBs) at target sites, and most DNA breakages induce mutations as small insertions or deletions (indels), by non-homologous end joining (NHEJ) repair pathway. However, for more accurate correction as knock-in or replacement of DNA base pairs, using the homology-directed repair (HDR) pathway is essential. Until now, many trials have greatly enhanced knock-in or substitution efficiency, by increasing HDR efficiency, or newly developed methods such as Base Editors (BEs). However, accuracy remains unsatisfactory. In this review, we summarize studies to overcome the limitations of HDR, using the CRISPR system, and discuss future direction.