Ecology reserves are the key regions relating to national ecology security. Diving into different protection regions and taking effective measures play an important role in ecological protection management in China. Evaluation of protection effect of nature reserves and coordinated management of different kinds of nature reserves is of great significance. This paper takes nature reserves and key ecological function regions in Jilin as study reasons, they are prohibited and restricted development areas respectively. This article analyses ecological space, vegetation ecology and water conservation services in different kinds of nature reserves, then evaluates and examines different management effects of these regions resulting from management gradient. According to protection effect of important ecological space, the highest area proportion of important ecological space in Jilin province was observed in nature reserves, and the lowest human disturbance index was found in the study area, which is positively correlated with the strict degree of management and control of ecological protection. However, the proportion of important ecological space area decreased from 1980 to 2015, and the extent of reduction was not positively correlated with strictness of management and control. Secondly, according to protection effect of vegetation ecology, the vegetation coverage gradually decreased from the east to the west, which is consistent with the spatial characteristics that the key ecological function areas and most of forest nature reserves are in the east, and the wetlands are in the west. However, due to the high area proportion of wetlands and water type nature reserves, and most of them are located at grassland and plain in the west, the annual variation of vegetation coverage in nature reserves is larger than that of the key ecological function areas, while the multi-year stability of vegetation coverage is lower than that of the key ecological function areas. Thirdly, in terms of protection effect of water conservation services, the water conservation services capacity in the east and west is higher than that in the middle of Jilin province. This is closely related to the fact that most of forests, grasslands and wetlands of Jilin are located in the east and west, and that the key ecological function zone and most of forest nature reserves are also in these areas. The water conservation capacity and its stability in nature reserves is better than those outside the reserves.