Caverns of Heaven and Places of Blessing (CHPB) are the earliest Ecological Reserve in China, but in recent years, due to the accelerated process of urbanization and weak protection, the Chinese traditional ecological reserve represented by CHPB has been damaged to a certain extent. How to accurately measure the dynamic changes of ecological value in existing ecological protection and construct is an initial topic of CHPB protection. To understand the temporal and spatial changes characteristics of biodiversity in CHPB, this paper selects three-time nodes in 1990, 2005, and 2020, and takes CHPB in Zhejiang Province as an example, comprehensive three influencing factors: habitat quality, landscape pattern, and nighttime-light. To provide a relevant theoretical basis for the protection of CHPB, this paper quantitatively analyzes the changes of ecological environment and biodiversity in recent 30 years. The results showed that from 1990 to 2020, the biodiversity of CHPB in Zhejiang Province showed a positive change, the decline in Caverns of Heaven overall area slowed down, and the core area rebounded. The spatial distribution change of biodiversity is highly consistent with the land-use changes. The low value regions of biodiversity are mainly concentrated in the regions with intensive human activities, and the area decreases with the expansion of construction land. The core areas are primary areas with high biodiversity and overlap with nature reserves, natural parks, Scenic and Historic Interest Area, and other protected areas. In a word, CHPB still plays a vital role in ecological and environmental protection. In the future development, we should still pay attention to its biodiversity protection, and give full play to its role in ecological and environmental protection, and realize the contemporary application of CHPB’s traditional ecological knowledge.