The complicated interaction between seepage field and stress field of tunnels in water-rich region has an important impact on the stratum deformation stability, structural safety performance, groundwater resources and ecological environment protection, etc. Especially for large-span urban tunnel with small spacing, the seepage funnels of the two holes will partially overlap and affect each other, making the seepage field distribution much more complex, and the difficulties in prediction water drainage and safety performance of supporting structure increase sharply. In this paper, in order to investigate the seepage field distribution and its influence on the structural mechanical behavior of small interval tunnel in water-rich region, using the self-developed seepage model test equipment, tests under different hydrostatic head heights were carried out on the Kexuecheng Tunnel, which is a typical small interval tunnel under complex hydrogeological environment in Chongqing, China. According to the test results, with the increase of buried depth and water level, the water pressure at each monitoring point gradually increased. For small interval tunnel, the average water pressure on the inner side decreased by 10–15 % compared with the outer side. Benefiting from the grouting circle can effectively block the supply of pore water in the rock mass, the water pressure behind the lining can be significantly reduced by 32 %–42 %. But with the increase of the hydrostatic height, the proportion of water pressure that can be shared by the grouting circle decreased gradually, and further aggravated the asymmetric distribution of the water pressure on lining structure. Meanwhile, the water pressure evolution curve shown a W-shaped distribution in horizontal direction and a V-shaped descend funnel along the tunnel axis, the predicted seepage influence range may increase to over 60–70 m under high water pressure. Contrary to the asymmetric distribution of water pressure, the earth pressure at the inner side was about 10 % higher than that at the outer side. Influenced by the tunnel excavation unloading effect, the closer to the tunnel face, the smaller the surrounding rock pressure. The minimum safety factors of the lining structure under water level of 0, 30, 40 and 50 m were 4.28, 3.85, 3.41 and 2.98, the structural safety performance significantly decreased with the increase of the hydrostatic head height.