Infertility impacts a substantial number of couples worldwide, and about 50% of cases are linked to male factors. The analysis of seminal fluid composition can improve diagnostic accuracy and offer deeper insights into the pathophysiology of male factor infertility. This study seeks to identify novel markers for diagnosing and treating male infertility by comparing organic acid profiles in the seminal fluid of individuals with normospermia, oligospermia, and azoospermia. Semen samples were collected from men with normospermia, oligospermia, and azoospermia. The organic acid profile in the seminal fluid was analyzed using liquid chromatography-mass spectrometry/mass spectrometry (LC/MS-MS). Data analysis was performed using SPSS and MetaboAnalyst. The study revealed significant differences in metabolite levels among normospermic, oligospermic, and azoospermic individuals. In groups with oligospermia, there were significant decreases in the levels of 2-OH-Isovaleric Acid, 3-Methyl-2-Oxovaleric Acid, Ethyl-Malonic Acid, Citric Acid, Oxoproline, Malic Acid, N-Acetyl-Aspartic Acid, Suberic Acid, Glutaconic Acid, and Succinic Acid. Similarly, individuals with azoospermia exhibited a notable reduction in the levels of Citric Acid, Malic Acid, and Suberic Acid. Furthermore, according to the Variable Importance in the Projection (VIP) score analysis, Ethyl-Malonic Acid, Glycolic Acid, and 3-Methyl-2-Oxovaleric Acid were identified as crucial factors for diagnosis and potential treatment strategies. The data obtained from the study highlights the significant potential of metabolites in assessing infertility and gaining a more in-depth understanding of the underlying pathological mechanisms.