Bay Area is a prominent symbol of world-class coastal cities, and ecological security is the basic guarantee of sustainable development of the Bay Area. This paper takes the Zhejiang Greater Bay Area as the research object, based on the ecological security evaluation results using Exploratory Spatial Data Analysis (ESDA) and Geostatistical Analysis (GA) to reveal the spatial correlation and heterogeneity of ecological security. Combing with the spatial characteristics of ecological security and the spatial distribution of land use management in the future and administrative units in Bay Area, the paper offers the differentiation strategy of ecological protection for the Zhejiang Greater Bay Area's economic and social development and ecological security to provide scientific support. The results showed that:(1) the spatial pattern of ecological security was "north-low and south-high", and the proportion of ecological security area was 71.7%. Overall ecosystem was safe. (2) The Moran'I value of ecological security reached 0.878, and the proportion of hot spot area was 50.65%, indicating the significantly positively spatial correlation. Structural variation dominated the spatial distribution of ecological security. Ningbo and Shaoxing were influenced by structural variation and random variation. Population density and industrial layout were the main random factors affecting the spatial heterogeneity of ecological security. (3) The urban development types were divided into optimization development zones, comprehensive development zones and ecological conservation development zones, among which the optimization development zones and comprehensive development zones were the vital areas for the economic development, and ecological conservation development area was the key area to ensure the ecological security of the Zhejiang Greater Bay Area. In the future, governments should adopt and implement the differentiated measures for ecological protection.