The invention discloses a systematic design method for long-distance vertically overlapped shield tunnels in a soft soil region, which comprises the following steps: determining an overlapped tunnel construction sequence, determining an optimal vertical net distance D0 and a minimum vertical net distance Dmin between an upper tunnel and a lower tunnel, obtaining a law of influence of the tunnel constructed later on the tunnel constructed first and surrounding strata, and making design schemes for tunnel risks under different net distance conditions. The invention systematically proposes the design method for the long-distance overlapped shield tunnels in the soft soil region for the first time, a vertical net distance control valve obtainment method is given, design schemes are made for different net distances according to the law of influence, and a systematic solution is provided for the design of overlapped shield tunnels in narrow underground space, and can be directly adopted in similar overlapped tunnel designs in the future.