Biodiversity is the basis for maintaining ecological balance and realizing ecological process and function. Northeast China is one of the most biodiverse areas in China and even the whole world. To understand the changes of the number and habitats changes of terrestrial vertebrates in the Northeast China, we combined long time-series species survey data and habitat remote sensing data, selected living planet index (LPI), area and fragmentation index of ecosystem types in different years as indicators, assessed the variation trend of terrestrial vertebrates and habitats in Northeast China in recent 40 years. The study showed the number of terrestrial vertebrate reduced by 70.1% from 1970 to 2010 in this area. The number of forest species reduced by 80.9% and the number of grassland and desert species increased by 180.9% from 1970 to 2010. The number of wetland species reduced by 75.7% from 1980 to 2010. The area of farmland and urban development increased by 25.2% and 32.3% from 1980 to 2015, respectively. With the continuous erode of natural ecological space such as reclamation of agriculture and urbanization, about 6.1% of the natural habitats were converted to artificial habitats. As a result, the natural habitats continued to decrease with a total decrease of about 8.0% in the area. The landscape fragmentation index of the natural habitat overall showed an increasing trend during 1980-2015. In particular, the index of fragmentation of forest habitats increased by about 42.7%, but the rising trend was lower after 2005, which was consistent with the decreasing trend in the number of vertebrate populations after 2005. This study showed that the number of large mammals in Northeast China has decreased sharply in the past 40 years, and the main reasons for this change are the increase in fragmentation of natural ecosystems and the decline of habitat quality caused by deforestation, population growth, urbanization, and traffic construction.