As the construction of ecological civilization has become a national strategy, the ecological space identification has become an important part of the contents of ecological protection in territory development plan. To promote regionally ecological protection, restoration and effective management, it is necessary to analyze and identify regional ecological security and restoration patterns. In this study, Habitat Quality module of InVEST Model is used to analyze Altay Prefecture's habitat quality changes in 1995, 2005 and 2018.We constructed regionally ecological security pattern from the perspective of ecological environment protection. The following conclusions were drawn.(1) From 1995 to 2018, the habitat quality in Altay Prefecture was at a medium level and showed a decrease trend which indicated that the local ecosystem had a continuous tendency of degradation. (2) Aiming to maintain systematicness of ecological structure and the integrity of ecological process, based on the morphological spatial pattern analysis (MSPA) combined with landscape connectivity method, there were fifteen ecological sources, which located in the north intermountain forest land and around Ulungur Lake. Thirty-eight effective ecological corridors with a length of about 2466km and about 80.08km² were identified which crossed among the grassland and forest in Altay Prefecture using Cost Distance toolbox of ArcGIS software. Fifty-two ecological nodes were mainly distributed in grassland and forest, which were identified at the intersection of least resistance paths and ecological corridors. (3) According to the habitat quality and the minimum cumulative resistance value, three types of crucial areas for ecological protection were classified, namely ecological conservation area, ecological maintenance area, and ecological breeding area. The research puts forward different ecological protection directions and proposes major tasks according to ecological-environmental problems in different crucial areas for ecological protection. The research provides different directions for ecological protection and restoration. Three ecological protection zones, which can offer references for identification of crucial areas and the comprehensive ecosystem protection and formulate sustainable development policies in Altay Prefecture.