In order to accurately assess the differentiation characteristics of canopy heat island intensity in highly complex megacity, taking Wuhan as an example, a calculation method for canopy urban heat island intensity (CUHII) that took into account the spatial differences in different urban areas was proposed, and combined with traditional algorithms based on the "urban suburban" dichotomy to explore the characteristics of urban heat islands under different algorithms. This study compared the diurnal variation characteristics and spatial distribution of CUHII between the two algorithms. Results showed that, the traditional algorithm consistently identified the urban heat island effects in all urban areas, with highly consistent diurnal variation curves among them. Conversely, in the regional algorithm, there were significant differences in CUHII variation in different regions, among which the Wuchang area with multiple large ecological spaces exhibited a continuous cold island phenomenon during the daytime. Moreover, except for sunny weather, heat weave and precipitation weather can significantly exacerbate the differences in CUHII in different regions under the new algorithm. Furthermore, the hot and cold island centers identified by the traditional algorithm were relatively small and located in the periphery of the central urban area, while the hot island center identified by the regional algorithm covered the central high-density development area through the city in a belt shape, and the cold island center was adjacent to the large natural lakes in the Wuchang area. These findings indicated that the new CUHII algorithm can weaken the interference of uneven development of urban areas on thermal environment assessment, which was conducive to in-depth exploration of heat island characteristics and more accurate identification of targeted areas that required priority intervention in urban thermal environment.