The Masson pine (Pinus massoniana Lamb.) has a relatively strong tolerance to stressors such as acid rain, drought, and phosphorus deficiency. Previous studies have mainly focused on morphological, physiological, and metabolic responses in the needles of the Masson pine. However, there has been little study of the effects of drought stress on root tip structure or the composition of volatile organic compounds (VOCs) in the root tip. Therefore, this work aimed to evaluate the VOCs and anatomical growth responses of Masson pine root tips to drought stress. The results showed that (1) drought stress inhibited increases in root biomass, root growth, and lateral root number, and damaged and significantly deformed the root apical structure; (2) the relative contents of monoterpenes decreased with the intensity of drought stress, but the relative content of sesquiterpenes increased. (3) The ratio of sesquiterpenes to monoterpenes in the root tip was approximately 1:2 in the absence of stress, and became 3:1 under severe drought stress. The results indicate changes of secondary metabolism in the root tip of the Masson pine in response to drought stress.