Nuclease based genome editing systems have been engineered as powerful tools to drive genomic alterations and enhance genome evolution via precise engineering in human and microbial cells. However, error-prone DNA repair has not been well studied to generate diverse genomic alterations and novel phenotypes. Here, we systematically investigated the interplay between DSB repair and genome editing tools, and found that modulating the DSB end resection factors could remarkably improve mutational efficiency and diversity without exogenous DNA template in yeast. Deleting SAE2, EXO1, FUN30, or overexpressing mre11-H125N for DSB end resection significantly increased the efficiency of CRISPR/Cas9 (more than 22-fold) and CRISPR/Cpf1 (more than 30-fold) -induced mutagenesis. Deleting SAE2 or overexpressing mre11-H125N diversified CRISPR/Cas9 or Cpf1-induced mutation 2~3-fold at URA3 locus, and 3~5-fold at ADE2 locus. Thus, the error-prone DNA repair factor was employed to develop a mutagenic genome editing (mGE) strategy, which increased the mutation types and effectively improved ethanol/glycerol ratio of Saccharomyces cerevisiae through diversified the expression of FPS1 and GPD1. Our results highlight the feasibility of reshaping the capability of genome editing by manipulating DSB repair factors and expand the application of genome editing in diversifying gene expression and enhancing genome evolution.