The invention provides a shallow depth excavation subway station separation open type structure and a construction method thereof and relates to the technical field of tunnel construction. The shallow depth excavation subway station separation open type structure comprises two separated symmetrically-arranged tunnels; secondary lining base plates are arranged at the bottoms of the tunnels, two secondary lining side walls are arranged above the two sides of each secondary lining base plate, horizontally-arranged middle plates and secondary lining arch parts are arranged on the middle portions and the tops of the secondary lining side walls correspondingly, arch part primary supports are arranged on the outer portions of the secondary lining arch parts, advance supports are arranged on the outer sides of the arch part primary supports, primary support large arch feet are arranged at the lower ends of the arch part primary supports, side wall primary supports are arranged below the primary support large arch feet, a plurality of pre-stressed anchor cables are arranged on each side wall primary support, and locking anchor pipes are arranged between the pre-stressed anchor cables; and base plate under layers and inverted arch primary supports are arranged below the secondary lining base plates. According to the shallow depth excavation subway station separation open type structure and the construction method thereof, an enough operation space and a high construction speed can be provided, and the purpose that rock stratum underground structure construction is conducted in a large mechanization mode is achieved.