Fine particulate matter (PM2.5) is related to embryo growth arrest (EGA). In this study, we collected demographic information from EGA cases and early pregnancy controls in Taiyuan, China, between 2022 and 2023 and obtained villi and serum samples from these participants. We employed multilevel mixed-effects logistic regression models to estimate the odds ratios (ORs). Subsequently, we examined the associations between PM2.5 and its components and the EGA-related biomarkers in the serum of the case-control groups. Additionally, we performed spatial metabolomics on villi using mass spectrometry imaging. Our results indicated that PM2.5 levels during pregnancy were higher in the EGA group compared to the control, increasing the risk by 17 % (OR=1.17, 95 %CI: 1.06-1.30, p = 0.001). PM2.5 and its components (Ni, Pb, ANY, NAP, ANT, PYR, and BaP) showed significant negative correlations with biomarkers (PAPP-A, VEGF, and PROG). Furthermore, EGA induced histopathological changes in the villi alongside differential spatial distribution of metabolites. Key metabolites, including 2'-deoxyinosine triphosphate, cytidine triphosphate, uridine triphosphate, guanosine-5'-triphosphate, guanosine diphosphate, and deoxyguanosine-5'-triphosphate, were predominantly involved in purine and pyrimidine metabolism pathways. It provides evidence of the association between PM2.5 and EGA and demonstrates the utility of spatial metabolomics in elucidating the metabolic alterations induced by PM2.5 in EGA.