Liliaceae Lilium is one of the most famous flower bulbs in the world. The root system bridges substance exchange between the soil and shoot and a strong root system supports the shoot growth and development. During growth, lilies develop two root systems: the basal root system and the stem root system. A few studies have currently reported the relationship between the growth of lily roots and shoots. In our study, we carried out a growth observation of lily shoots (stem and leaves) and underground parts (bulb, basal roots, and stem roots) by cutting the basal roots, stem roots and bulbs of lily. We also discussed how these treatments affected the growth of lilies. The results indicated that both bulb weight and bulb volume showed an initial decreasing and a subsequent increasing trend during growth, and the bulb weight could better reflect bulb nutrient dynamics compared with the bulb volume. The trend in bulb weight was the opposite to that of shoot weight; the bulb weight decreased at first and then increased, whereas the shoot weight first increased and decreased afterward. The turning points for both variations occurred just at the time of flowering. The variation of plant heights showed a typical S-curve and the time where plant heights entered rapid growth coincided with the time where the stem root system started to emerge. The stem root system only took 10 days to complete development. The biological significance was that after plantation, nutrients supporting the growth of the shoots is mainly supplied and maintained by the bulbs and they should be transferred to the stem roots in the shortest delay possible. During early emergence of the stem root system, substance consumed from the bulb are mainly used for the formation of stem roots and after the number of leaves has become stable, substances supplying the shoot growth are mainly from soil nutrients absorbed by the stem roots. The stem root system plays a key role in the growth and development of lily shoots, whereas the basal roots and the bulb would not affect lily growth to a significant level.