Some problems exist in the existing specifications and design of drainage system of highway tunnel with permafrost. Hence, the freezing damage of highway tunnels with permafrost layer is investigated; the potential problems in current codes and design are analyzed by considering different types of permafrost sections that highway tunnels pass through in permafrost region; and segmentation design of drainage facilities in different types of permafrost sections of highway tunnels with permafrost layer and connecting technology between sections are proposed. The results show that: (1) The drainage systems of highway tunnel sections vary due to different burial depths and different types of permafrost layers. (2) The drainage systems of different permafrost sections should be connected with each other, and should be rationally selected according to the tunnel slope. (3) The water at the connection between permafrost section and nonpermafrost section can be directly discharged through underground drainage ditch or along the tunnel axis by considering the mountain topography or spacing between left and right lines.