As an important industrial and grain production base of China, livestock and poultry industry have been rapidly developed in the northeastern provinces. With the rapid increasing amount of animal production, how to handle the huge amount of animal manure has become a critical issue for local government. A quantitative analysis based on geographic information system (GIS) combining the biophysical, environmental, social and economic factors was applied to determine the land suitability for manure application in the northeastern provinces. The results show that a farmland area of 211942.7 km2, accounting for 78.9% of the cultivated land in three northeastern provinces, is estimated to be suitable for manure application. The suitable farmlands are mostly distributed in Heilongjiang and Jilin provinces. Proximity to residential area, water body and roads are identified as the primary factors influencing the manure application, while rainfall is the main factor to generate discrepancies in different areas. Furthermore, the future potential capacity for animal production in three provinces was forecasted based on the areas of suitable land and the population of existing livestock production. Among 36 cities of three provinces, the big variation is observed, Siping City is overproducing 1.813 million heads of pig unit at present, but Qiqihaer City still has the potential to rear 11.203 million heads of pig unit. Overall, eastern region of the study area holds the high potential for animal production with a surplus capacity of 2.842 million heads of pig unit, the potential of the typical mountain and forest areas is only 10% of eastern region, however. In contrast, in half of western region (central Liaoning province and central Jilin Province), their animal populations have exceeded the land carrying capacity. Therefore, we strongly suggest a site-specific animal production and manure application guide to achieve a sustainable development of livestock production in the northeastern provinces.