It has been reported that fruit cultivars could be detected by using near-infrared spectroscopy. Therefore, it is doubted that the optical properties (OPs) have differences among different fruit cultivars. However, it is not clear the difference in OPs and whether there is a difference in the relationship between OPs and internal quality. To answer these questions, four kiwifruit cultivars in two species, i.e., ‘Hayward’ and ‘Xuxiang’ of Actinidia deliciosa and ‘Huayou’ and ‘Hongyang’ of Actinidia chinensis, were selected as representative samples to obtain OPs (absorption coefficient μa and reduced scattering coefficient μs') of pulp and peel in storage and 950–1650 nm using an integrating sphere system. Then the relationship between the OPs and internal quality (soluble solids content (SSC), moisture content, and firmness) and microstructure were analyzed. Moreover, the optical parameter with greater potential in classifying kiwifruit cultivars was investigated. The results showed that the changes in μa and μs' with time differed among the four cultivars. Significant differences in the values of μa and μs' were noted among the four cultivars at some given times. For a given species, the investigated two cultivars had an obvious difference in OPs. Below about 1400 nm, the pulp’s μa of ‘Hayward’, ‘Huayou’, and ‘Hongyang’ was positively correlated with SSC and negatively related to moisture content and firmness, and the correlation coefficients changed little with wavelength. However, the correlation coefficients changed greatly for ‘Xuxiang’. Kiwifruit cultivars affect OPs and their relationship with the internal quality. The modeling results of the linear discriminant analysis showed that the μa had greater potential than μs' in identifying kiwifruit cultivars. The study provides useful information for identifying fruit cultivars and internal quality by using near-infrared spectroscopy technology.