Haploid mammalian embryonic stem cells (haESCs) serve as a powerful tool for genetic analyses at both cellular and organismal levels. However, spontaneous diploidization of haESCs limits their use in these analyses. Addition of small molecules to culture medium to control the cell cycle can slow down diploidization, but cellsorting methods such as FACS are still required to enrich haploid cells for long-term maintenance in vitro. Here, acting on our observation that haploid and diploidized cells differ in diameter, we developed a simplified filtration method to enrich haploid cells from cultured haESCs. We found that regular cell filtration with this system reliably maintained haploidy of mouse haESCs for over 30 passages. Importantly, CRISPR/Cas9-mediated knockout and knockin were successfully achieved in the filtrated cells, leading to stable haploid cell lines carrying the desired gene modifications. Of note, by injecting the haESCs into metaphase II oocytes, we efficiently obtained live mice with the expected genetic traits, indicating that the regular filtration maintained the functional integrity of the haESCs. Moreover, this filtration system was also feasible for derivation of mouse haESCs from parthenogenetic haploid blastocysts and for human haESCs maintenance. In conclusion, we have identified a reliable, efficient and easy-to-handle technique for countering diploidization of haploid cells, a major obstacle in haESC applications.