In order to deeply study the treatment method of highway cutting slope instability under the condition of expansive soil covered with rock layer in alpine region, based on the unstable slope project of Zhang Shang Expressway, the comprehensive treatment method of slope under this bad geology is put forward. The governance protection structure consists of rigid protection system, drainage system, thermal insulation system, flexible protection system and waterproof system. The rigid protection system is an anti-slide pile, which is set at the height of 1/3 of the first grade slope, and its parameters are calculated by cutting the slope of the rock layer in the unstable area to reduce the required anti-slide force of the remaining soil; The drainage system consists of built-in tilting drainage pipes between rock layer and expansive soil layer, gravel drainage layer outside expansive soil layer after excavation of soil in unstable area, horizontal drainage pipe in gravel layer, drainage ditch, intercepting ditch and side ditch of each platform; The thermal insulation system is a backfill soil layer and a cultivated clay layer arranged outside the gravel layer; The flexible protection system is a geogrid in the thermal insulation soil layer; The water-proof system consists of two cloth and one membrane water-proof layers planted under the clay layer on the backfill soil platform, and two cloth and one membrane water-proof layers in the contact area between the gravel layer and the anti-slide pile. The field treatment results show that this method can effectively prevent the slope from instability and failure again. The research results can provide reference for the treatment of similar slopes under expansive rock and soil in alpine region.