Objective <p>This study aimed to identify potential susceptibility loci for testicular germ cell tumors (TGCT) through a comprehensive multi-omics analysis.</p> Methods <p>A Mendelian randomization (MR) analysis was conducted to investigate the causal relationships between immune cell phenotypes and TGCT. Summary-based Mendelian Randomization (SMR) and colocalization analyses were subsequently performed to examine candidate phenotypes and TGCT using quantitative trait locis from multiple datasets. Differential gene expression analysis was employed to explore the immune landscape of the target gene in the TGCT tumor microenvironment using UCSC databases. Additionally, potential pathway mechanisms were investigated to elucidate the functional role of candidate genes.</p> Results <p>MR analysis identified a significant causal association between the immune cell phenotype HLA-DR on monocytes and TGCT (<i>p</i> = 0.02). SMR analysis revealed that BDH2 was significantly associated with TGCT susceptibility (OR = 0.597, <i>p</i> = 2.21e-07). Colocalization analysis suggested shared genetic variation between BDH2 and TGCT (PP.H4 = 0.95). Immunohistochemistry staining confirmed that BDH2 mRNA levels were significantly lower in TGCT tissues than in normal controls (<i>p</i> &lt; 0.001). In the TGCT tumor microenvironment, lower BDH2 expression was associated with higher immune scores, with T cells and B cells predominantly enriched in the low-expression group, whereas monocytes and endothelial cells were more abundant in the high-expression group. Furthermore, members of the HLA family, exhibited significant correlations between their methylation levels and low BDH2 expression groups. Pathway analysis indicated that BDH2 may influence TGCT progression through the RAS-MAPK signaling pathway.</p> Conclusions <p>Our findings support a significant susceptibility relationship between the phenotype HLA-DR on monocytes, BDH2, and TGCT.</p>