The invention discloses a heavy haul railway tunnel bottom structure design method considering a train long-term effect. The method comprises the steps that firstly an initial value of a design parameter of a tunnel bottom structure is determined according to relevant norms and engineering experience, then a train-track-tunnel integral numerical value model is adopted to calculate stress distribution and a strain ratio value of the tunnel bottom structure on the condition of the design parameter, a numerical value calculation method based on a damage model is adopted to obtain power damage of the tunnel bottom structure caused by a single-time train effect, further, a nonlinear cumulative damage model is adopted to calculate a cumulative damage value at a key position of the tunnel bottom structure, the cumulative damage value obtained by calculation and critical damage of the tunnel bottom structure are compared, when reaching a critical damage index, the calculation result is the design parameter of the tunnel bottom structure, when the difference is big, the design parameter is adjusted, and the calculation is reconducted according to the steps until the final design parameter is obtained.