Optimal sperm DNA integrity is essential for fertilization and embryo health. Research indicates that testicular sperm (TS), obtained via TESA or TESE, typically show lower sperm DNA fragmentation (SDF) than ejaculated sperm after standard abstinence. Shortening abstinence to less than 2days might reduce SDF, offering a less invasive and more cost-effective alternative to surgical sperm retrieval. Yet, no studies have directly compared the efficacy of shorter abstinence against TS extraction for lowering SDF. Our meta-analysis aims to address this gap by comparing SDF levels in TS to those in ejaculated sperm after a short abstinence period. Meta-analysis of 16 randomized controlled and prospective observational studies included 4 on TS and 12 on short abstinence ejaculation. The meta-analysis followed MOOSE guidelines, scrutinizing databases including Cochrane Library, Web of Science, Embase, MEDLINE(R), and PUMBED up to November 16, 2023. The analysis was conducted using RevMan. The observational studies' methodological quality was assessed using the Newcastle-Ottawa Scale, and the overall evidence quality was evaluated following the GRADE criteria. To compare short ejaculation duration and TS (are not directly compared in the literature) for SDF levels, we analyzed relevant data from studies of each method. We adjusted the participant numbers in the TS group by 1/3 and included each TS study three times, to perform a comparison against the short duration studies which were in a ratio of 1:3. This approach maintained an unaltered cumulative subject count for the meta-analysis of TS studies. A total of 641 patients were included, comprising 120 and 521 patients with SDF measurements following TS and ejaculation after a short abstinence period, respectively. The studies had varied inclusion criteria, with not all patients having an initial elevated SDF. Some studies had incomplete details on age and other demographics. However, the mean ± SD age of 93 TS patients was 38.15 ± 5.48 years vs. 37.7 ± 6.0 years of 444 short abstinence patients, demonstrating no significant difference (P = 0.544). Short abstinence durations ranged from 1 to 48h. Diverse DNA fragmentation tests were used: TUNEL assay in three testicular sperm studies, SCD assay in one, and in the short abstinence group, four used TUNEL and six used SCD assays, along with one each using SCSA and Halosperm. The mean ± SD SDF was lower in the TS group than in the short abstinence group (mean difference - 9.48, 95%CI -12.45 to -6.52, P < 0.001, I2 = 85%). Sensitivity analysis revealed that no single study significantly influenced the results. Employing the GRADE criteria, the initial assessment categorized the overall quality of evidence as low due to the observational nature of the acquired data. All studies were of medium to high quality. This study suggests testicular sperm may be better than ejaculated sperm for improving SDF in infertility cases. Direct comparisons are needed, before deeming short abstinence less effective. Future research should directly compare reproductive outcomes using both methods.