Background: Sperm DNA fragmentation (SDF) may hinder embryonic development and growth, increasing the risk of spontaneous miscarriage, and is considered an important factor affecting male infertility (MI). Traditional Chinese herbal medicine is considered effective in the treatment of MI due to SDF by nourishing kidney essence or promoting blood circulation for removing blood stasis. The objective of this systematic review protocol is to evaluate the effectiveness and safety of traditional Chinese herbal medicine on the treatment of MI associated with SDF. Methods: We searched the PubMed, Embase, Web of Science, Cochrane Library, CNKI, VIP Chinese Science, Technology Journal Database, and Wanfang Database until the end of 2020 for English and Chinese published literature. Randomized controlled trials (RCTs) to evaluate the effectiveness and safety of traditional Chinese herbal medicine for the treatment of MI associated with SDF will be included. Study selection and data extraction were performed independently by 2 reviewers, and the quality evaluation and risk assessment were assessed by the Cochrane collaboration's tool, and use the RevMan 5.3 software for meta-analysis. Conclusion: This study will evaluate the efficacy and safety of traditional Chinese herbal medicine for the treatment of MI due to SDF, which may provide some help for the clinician's decision. Prospero registration number: CRD42020221053.