The north-south transitional zone in China mainly consists of the Qinling-Daba Mountains. It is the most important West-East geo-ecological space in China, containing protected areas vital for biodiversity conservation and ecological security of China. The protection and rational development of its natural habitat is of great significance to China’s ecological security and integration of protected areas based on mountain forest ecosystems on a global scale. In this study, five important types of protected areas in the transitional zone were selected, and their spatial patterns were analysed. Spatial analysis methods, such as kernel density estimation and accessibility analysis, were employed for both point and areal data, and focused on four aspects: land use scale, shift in the centre of gravity, spatial agglomeration, and accessibility. In addition, policy background and evolution of spatial and temporal characteristics of the protected area system in the transitional zone from 1963 to 2017 were also examined. We analysed the characteristics and geographical significance of the West-east corridor using the spatial pattern of the protected area system from the perspective of ecological and economic spaces. We focused on spatial shape, type intersection, and key areas to analyse the spatial overlap of the protected areas. Protected area establishment was divided into three stages: initial (1956–1980), rapid development (1981–2013), and national park transformation (2014—present). These stages reflected the change in the concept of ‘simple protection—sustainable use—integration and upgrade’ for protected areas of China. The spatial centre of gravity of the protection zone system was located in the west Qinling-Daba Mountains, and its high-density core exhibited a relatively stable N-shaped structure composed of four gathering areas. Affected by factors such as geographic environment and socio-economic development density, the average access time for protected areas was high (1.56 h); wetland parks and scenic areas are located closer to the city centre. As the West-east corridor in the transitional zone extends from west to east, there is a clear spatial dislocation between the development of protected areas and the intensity of human activities. During development, differentiated goal orientation should be adopted based on the idea of zoning and classified governance. With the advancement of the construction of protected areas, the spatial overlap of protected areas in the transition zone has become more prominent. At present, the spatially overlapped protected areas in the transitional zone remain prominent, with inclusion overlap being the most common, and forest parks exhibiting the highest probability of overlap with other protected areas, we should focus on in the integration process of the corridor-type ecological space based on the mountain forest ecosystem.