Previous diffusion tensor imaging (DTI) studies had investigated the white matter (WM) integrity abnormalities in smokers. Exposure to nicotine disrupts neurodevelopment during adolescence, possibly by disrupting the trophic effects of acetylcholine. However, little is known about the diffusion parameters of specific fibre bundles at multiple locations in young smokers. Thirty-seven young smokers and 29 age-, education- and gender-matched healthy non-smokers participated in this study. Automated Fibre Quantification (AFQ) was employed to investigate the WM microstructure in young smokers by integrating multiple indices. Diffusion parameters, that is, fractional anisotropy (FA), axial diffusion (AD), radial diffusion (RD) and mean diffusion (MD), were calculated at 100 points along the length of 18 major brain tracts. The relationships between neuroimaging differences and smoking behaviours were explored, including Fagerström Test of Nicotine Dependence (FTND) and pack-years. Compared with non-smokers, young smokers showed significantly increased FA, AD and decreased RD in the left uncinate fasciculus (UF) and right thalamic radiation (TR), increased AD, RD and decreased FA in the right arcuate fasciculus (Arc). Correlation analyses revealed that FA values of the left UF and RD values of the right Arc were negatively correlated with FTND score in smokers and FA values of the right Arc were positively correlated with FTND scores. Positive correlation was observed between AD values of the left UF and pack-years in smokers. The findings enhanced our understanding of the potential effect of adolescent smoking on WM microstructure.