Abstract: The 1-year-old seedlings were used as the research materials to disclose the response of root morphology of Pinus yunnanensis seedlings to stumping heights in this study. The study was conducted by pot experiment in greenhouse and three stumping heights (5, 10 cm and 15 cm) with control were set up. After one growth season root morphological characteristics and biomass of P. yunnanensis seedlings were measured and analyzed. The results showed that, except for the average diameter and the ratio of main root biomass to lateral root biomass, other root morphological indicators in the stumping treatment were higher than those in the control, that is, the stumping can promote root growth. There were different responses on stumping heights for different root morphological characteristics and biomass indexes. The total root length, surface area, total root volume and lateral root biomass decreased with the decreasing of stumping height. The major root length, average diameter, major root biomass and the ratio of root biomass to aboveground biomass increased with the decreasing of stumping height. The root biomass first increased and then decreased with the decreasing of stumping height. Based on the coefficient of variation of the measured indexes, stumping treatments decreased when compared with control. Except for control, the coefficient of variation for those indexes increased with the decrease of stumping height. Correlation analyses showed that the indexes were interacted with each other. Further analyses showed that the stumping changed lightly allometric growth relationship between the aboveground biomass and root biomass, lateral root biomass and major root biomass, root biomass and individual biomass. In conclusion, growth resources were shifted to the underground part after stumping, that is, the aboveground biomass accumulation decreased with the decreasing of stumping height. For the redistribution of the underground part biomass, the major root was invested preferentially, and major root length and major root biomass increased to adapt to a growth needs after stumping.