Using high-performance liquid chromatography, we examined the relationship between the content of endogenous hormones (zeatin [ZT], gibberellic acid [GA₃], indole acetic acid [IAA], abscisic acid [ABA]) during fruit growth and development in Lycium barbarum Ningqi 1 and Ningqi 5. The diameter, length, and single-fruit weight were greater in Ningqi 5 than Ningqi 1; the early stage of fruit development, especially in the slow growth period, was a critical period for Ningqi 5 and could increase fruit size and weight. In Ningqi 1, IAA content in seeds was positively correlated with diameter and single-fruit weight and length. In Ningqi 5, ZT content in pericarp and IAA content in seeds was positively correlated with diameter and single-fruit weight. ZT can promote cell division, and in fruit growth, the cell number is more important than the cell size. In the slow-growth period (8–25 d), the content of ABA in the pericarp and seed was lower in Ningqi 5 than Ningqi 1, which explains the greater diameter, length and single-fruit weight of Ningqi 5 than Ningqi 1. The changes in GA₃ and cellulase (Cx) were opposite, which indicated that Cx activity was inhibited by the high content of the pericarp GA₃ in prophase and metaphase in Ningqi 1, thus showing fruit swelling. The changes of IAA in pericarp and polygalacturonase (PG), pectinesterase (PE), ZT and PE, ABA and Cx, ZT in seeds and PE were opposite. As well, in prophase and metaphase of Ningqi 5, the high content of IAA, ZT and ABA in the pericarp and ZT in seeds could promote fruit expansion, which explains the larger fruit size in Ningqi 5 than Ningqi 1. In Ningqi 5, ZT content in the pericarp and IAA content in seeds could enhance the activity of Cx. In Ningqi 1, ABA content in the pericarp could enhance the activity of PE, then promote the maturation of fruit.