Severe air pollution in China has caused significant tourism transformation for pursuing fresh air in microclimate tourism markets. Contemporary practices simply measure the air freshness of destinations and scenic spots using a single index, i.e., primarily negative oxygen ions (O2−). This index cannot comprehensively reveal scenic spots’ air freshness degree and determine the dynamic interactions between air freshness and scenic spots’ tourism development, thus inducing an illusion of air freshness for the target scenic spots. Meanwhile, the current fresh air index primarily ignores connections with the microclimate index of scenic spots and cannot provide a multidimensional index for scenic spots to take advantage of both air and microclimate resources for diverse tourism products and service production. Therefore, this study proposes a multidimensional index, the fresh air–natural microclimate comfort index (FAI-NMCI), connecting the fresh air index with the natural microclimate comfort index of scenic spots together from transdisciplinary and multidisciplinary perspectives. This study utilizes FAI-NMCI to measure four scenic spots of Fujian Province, and reveals in-depth results of scenic spots’ air freshness and natural microclimate comfort degree together. The results demonstrate that the four scenic spots in Fujian province of China had different levels of air freshness degree and natural microclimate comfort degree in 2018. The natural scenic spots were mostly distributed in Healing Fresh, Very Fresh, and Super Fresh levels of FAI with the most comfortable and comfortable levels of NMCI. The cultural scenic spots were mostly distributed in Relatively Fresh and Healing Fresh levels of FAI with the most comfortable and comfortable levels of NMCI. Meanwhile, the FAI-NMCI of natural and cultural scenic spots also had significant differences within 24 Jieqi, which will promote dynamic and creative utilization of those resources in microclimate tourism development.