Scientific implementation of ecological protection and restoration engineering in "mountains-rivers-forests-farmlands-lakes-grasslands System (MRFFLGs)" is a way for the construction of China's ecological civilization and also an important measure to solve the ecological and environmental problems. This article analyzes the ecological service value, ecosystem quality, and ecological function stability of ecosystems based on ecological characteristics and functions of MRFFLGs. The ecological network is constructed by the minimum cumulative resistance model based on the ecosystem and topographical features of the Irtysh River Basin. Combined with the identification of degraded ecological source areas, the complete and functional ecological structure is completed throughout the basin. The results indicated that (1) the decrease in the ecological service value and ecological quality of this basin was mainly caused by the decline of forest vegetation coverage resulted from human disturbance. (2) There was 20.67% of this basin with a serious deterioration of ecological quality, and the corresponding restoration was urgently needed. (3) The ecological source area of the basin presented a pattern of "west-to-southeast extension, alternating northeast to southwest". This ecological source areas combined with the 21 ecological corridors and 9 key ecological nodes constructed by the study formed the whole basin ecological pattern. (4)The basin should be ecologically protected and repaired in the manner of enhancing ecological function in the north, maintaining ecological security in the middle and sealing ecological environment in the south. (5) The ecological protection and restoration based on local conditions should follow the natural law, pay attention to the overall protection and system restoration of the MRFFLGs-Human being, and insist on the management of human activities and the protection and restoration of ecosystems.