Abstract Study question To evaluate the association between sperm DNA fragmentation measured by two new SCD-based assay and sperm parameters as well as ART outcomes. Summary answer Sperm DNA fragmentation assessed by novel sperm DNA fragmentation assay is significantly negative correlated with semen parameters and embryo quality. What is known already Sperm DNA fragmentation (SDF) is one of the major defects in sperm chromatin. This may lead to male infertility, abnormal embryological development, and pregnancy loss. To date, SDF testing has emerged as a means of diagnosis in some medical institutions as an additional assessment for predicting fecundity and guiding treatment regimen. Assisted reproductive technology (ART) such as IVF and ICSI have played a pivotal role in the treatment of infertility over two decades. However, a parts of patients with high level of SDF underwent ART may still have poor clinical outcome. Study design, size, duration A total of 200 participants was included in this prospective cohort study. Data was collected from the reproductive medicine center from June 2020 through December 2021. Participants/materials, setting, methods This study included 200 infertile couples attending for assisted reproductive treatment. Semen sample collected on the day of fertilization was analyzed for SDF by using LensHooke® R10 (R10) and LensHooke® R11 (R11) kits. Semen analysis parameters, embryologic outcome, and clinical outcome after ART treatment were compared between groups with low-level SDF and high-level SDF. Main results and the role of chance The SDF assessed by R10 was negatively correlated with sperm total motility (Spearman's ρ=-0.24,P=0.0007). The SDF assessed by R11 was negatively correlated with sperm concentration (Spearman's ρ=-0.26, P = 0.0002), total motility (Spearman's ρ=-0.45, P < 0.0001), progressive motility (Spearman's ρ=-0.29, P < 0.0001), and normal morphology (Spearman's ρ=-0.43, P < 0.0001). Moreover, SDF obtained by the R10 in asthenozoospermic (26.9% ± 19.5%, p < 0.05) was significantly higher than that in normozoospermic samples (14.8% ± 8.9%). SDF obtained by the R11 in oligozoospermic (21.1% ± 17.9%,p<0.01), asthenozoospermic (25.3% ± 19.4%, p < 0.001), teratozoospermic (17% ± 13.2%, p < 0.01), and oligoasthenoteratozoospermic samples (35.6% ± 24.5%, p < 0.0001) were significantly higher than that in normozoospermic samples (7.9% ± 4.2%). In addition, there was significant difference in good embryo rate post IVF between the groups of low SDF (< 14%) and high SDF (≥ 14%), as measured by R11. Limitations, reasons for caution To focus on male factor-related infertility, the female partner with an age above 38 years old was not enrolled, however, other female factors were not precluded from this study. Wider implications of the findings Sperm DNA fragmentation has proven to be a valuable biomarker in male fertility evaluation, while its significance as a predictor of clinical outcomes following ART requires further investigation. Trial registration number CS2-20012