Asymmetric large deformation disasters inevitably occur when highway tunnels cross active fault zones. Relying on the Nanlangshan No.1 Tunnel Project, the mechanism of asymmetric deformation is analyzed based on the in-situ engineering geology and tunnel monitoring data, and numerical calculations are used for verification. Based on the results of asymmetric large deformation disaster analysis, the control scheme of double-layer primary support is proposed, and the design is optimized with numerical calculation before engineering practice. The conclusions are as follows: 1. The original primary support program cannot withstand the asymmetric surrounding rock pressure, and the slip of the weak interlayer in the engineering geology is the main reason for the asymmetric deformation disaster in the tunnel. 2. According to the results of the numerical calculations, the tilted weak interlayer greatly reduces the stability of the surrounding rock, which leads to the local bending damage in the left shoulder of the tunnel, and the local shear deformation damage in the right arch girdle. 3. When using the double-layer primary support program, the appropriate delay of support timing for the second layer of primary support can effectively decrease the tunnel asymmetric deformation. However, if the second layer of primary support lag distance is too large, it will also lead to tunnel deformation convergence larger, or support failure and other issues. So, it is recommended that the second layer of primary support lags behind the first layer of primary support by 2 m to be applied.