The bacterial CRISPR-Cas9 system has emerged as an effective tool for sequence-specific gene knockout through non-homologous end joining (NHEJ), but it remains inefficient for precise editing of genome sequences. Here we develop a reporter-based screening approach for high-throughput identification of chemical compounds that can modulate precise genome editing through homology-directed repair (HDR). Using our screening method, we have identified small molecules that can enhance CRISPR-mediated HDR efficiency, 3-fold for large fragment insertions and 9-fold for point mutations. Interestingly, we have also observed that a small molecule that inhibits HDR can enhance frame shift insertion and deletion (indel) mutations mediated by NHEJ. The identified small molecules function robustly in diverse cell types with minimal toxicity. The use of small molecules provides a simple and effective strategy to enhance precise genome engineering applications and facilitates the study of DNA repair mechanisms in mammalian cells. Display omitted •Screening identifies small molecules that modulate CRISPR genome editing•Small molecules enhance precise genome editing via HDR•Small molecules also enhance sequence-specific gene knockout via NHEJ•The identified small molecules work for different genes in diverse cell types From a high-throughput screen, Yu et al. identify small molecules that modulate CRISPR-Cas9-mediated genome editing in human stem cells, for insertions, precise genome editing, and gene knockouts.