Objective: To study the impact of vitamin B12, folic acid (FA) and methylmalonic acid (MMA) on sperm parameters; count, motility and morphology leading to male fertility. Methods: The cross-sectional study comprised of one hundred and eighty-six subjects with normal sperm parameters (fertile) and 88 subjects with abnormal sperm parameters labelled as “infertile” from a sample population of Karachi, Pakistan. Vitamin B12, FA and MMA levels in serum were analysed by enzyme linked immune sorbent assay. Unadjusted and adjusted prevalence ratio with their 95% CI were reported by using cox regression algorithm to assess the association of Vitamin B12, FA and MMA and other factors with male Infertility. Unadjusted and adjusted beta coefficients with 95% CI were reported by using linear regression analysis for assessing relationship of Vitamin B12, FA and MMA and other factors with semen parameters (count, motility and morphology); P value of <.05 was considered significant. Results: It was declared that with every 1 unit increase in vitamin B12, FA and MMA the prevalence of infertility was decreased by 1%, 17% and 74%, respectively. Multivariate analysis revealed that vitamin B12, FA and MMA had a significant association with total sperm count, motility and morphology. The sperm parameters were also affected by increase in; LH, BMI and body fat %. There was a significant positive correlation of; LH with Vitamin B12 and FA (0.423 < 0.001, 0.338 < 0.001) and testosterone with vitamin B12 and FA (0.326 < 0.001, 0.291 < 0.001), respectively. Conclusion: All the studied micronutrients; Vitamin B12, FA and MMA had a positive effect on sperm parameters; count, motility and morphology and the associated reproductive hormones which explains their role on reproductive functions required to acquire fertility.