With the rapid development of economy and urbanization in China since the Reform and Opening-up in 1978, the living and industrial spaces have been occupied by numerous ecological space. Therefore, it calls for an overall evaluation of ecological space changes in the background of ecological civilization construction. First, the ecological space classification was built and corresponded to the land use classification system referring to the definition of ecological space. Then, the spatio-temporal characteristics of ecological space changes between 1990 and 2015 were examined. The results indicated that the areas of ecologically-used land across China decreased continuously in 1990-2015, mainly transformed to semi-ecologically-used land, which occurred in major grain production areas and surrounding areas. The areas of semi-ecologically-used land fluctuated significantly, which was expanded in the early stage, then converted into weak-ecologically-used land in the latter stage. Relating to the acceleration of urbanization, weak-ecologically-used land continued to expand. The turning point of ecological space transformation showed certain regional differences, showing a three-level gradient from east to west and from south to north. As a result, regionally ecological space conditions shows a strong correlation with economic development strategies and ecological space governance. This study has important implications for the formulation of nationally ecological space control near-and long-term strategic plan. The study suggests that different regions within varied gradients should consider bottom line of ecological space security and its governance based on the transformation stage and its driving mechanisms.