Human hair has become a promising non-invasive matrix in assessing exposure to environmental organic pollutants (OPs). However, exogenous contaminants, which were absorbed into the hair via sweat, sebum, and air particles/dust, could contribute to OP levels in hair and interfere with the precise exposure assessment. So far, the microscopic mechanisms underlying the absorption of exogenous OPs into hair remain inadequately understood. This study focused on the in-situ investigation of the diffusion processes of exogenous OPs into the hair structure using secondary ion mass spectrometry (SIMS) and isotopic tracer techniques. Results showed that the relative signal intensities of deuterium-labeled tris(1,3-dichloro-2-propyl) phosphate (TDCPP), 1-hydroxypyrene (1-OH-Pry), and bisphenol A (BPA) in the hair cortex were notably elevated after a 6-hour exposure. Diffusion coefficients of contaminants were related to their molecular weight, and absorption volumes to their water solubility and molecular structures. Exposure duration and solvent influenced the rate of diffusion and absorption volumes. The distribution of deuterium-labeled molecules in exposed hair samples after washing with two different solvents (acetone or water) was similar to that before washing. Our findings revealed the diffusion of OPs in hair cross-sections, indicating exogenous contributions to contaminants that are biologically incorporated into the hair.