Light-emitting diodes (LEDs) are known to affect plant morphology. In this study, we examined the relationship between changes in stem and root morphology in Populus sieboldii × Populus grandidentata induced by irradiation with blue (450 nm), red (630 nm), and white (combination of red, blue, and green; 525 nm) LED lights. Populus samples were reared for 36–55 days in separate LED incubators, and changes in their appearance were observed. After rearing, the main stem of each seedling was cut, leaving a section of stem extending from the roots to ≈20 mm above the medium surface; this part was used for tensile testing. The tensile tests were performed to clarify the relationship between the tensile force and displacement until 100 mm. Irradiation with blue light produced the tallest seedlings. The highest dry weight (root and stem) and largest stem diameter were obtained under red light. The results of the tensile tests showed that the work required to displace seedlings 100 mm was highest in plants reared under red light, followed by white and blue light. Numerous root branches developed under red light, and taproots were longest in saplings reared under blue light. The observed differences in root system morphology that were induced by rearing under light of different wavelengths were reflected in the tensile force required to extract the trees from the medium. The morphological changes observed in roots are important given the role of roots in forests after landslides, earthquakes, and other disruptions.