The root of Paeonia lactiflora Pall. is widely used in the pharmaceutical, food and cosmetic industries. For these purposes, roots are graded according to diameter, with larger roots considered to be of better quality. To assess the inherent quality of different grades and of different tissues in roots of P. lactiflora, here laser microdissection coupled with UPLC-Q/TOF–MS was applied. The results show the quantity of pharmaceutically important components decreased with increase in root diameter from 0.3 cm to 0.7 cm. Above 0.7 cm of diameter, quantity and diversity of these components increased proportionally with increase in root diameter. The tissue-specific study indicated that the high content of paeoniflorin and albiflorin are mainly distributed in the cork and cortex. According to the results of this study, the roots of P. lactiflora greater than 1.7 cm in diameter are of better quality medicinal use than smaller, and the commercial grades chose was best cutoff points. The fine roots and the outer bank of roots, which besides the commercial grades, contain such significant amounts of chemical components too. This study provides a new and practical method for evaluating the different grades of P. lactiflora.