In order to investigate the influencing factors of the mechanical properties and the microscopic pore structure of fly ash based geopolymer mortar, the curing temperature, high temperature curing time, water phase content z, water glass modulus n, solution/cement ratio R and the cement/sand ratio J were studied by orthogonal design and single variable method, respectively. And its mathematical model was proposed. The relationship between microscopic pore characteristics and mechanical properties of mortar was analyzed by Mercury intrusion porosimetry (MIP). The results show that: Increasing the curing temperature can significantly increase the compressive strength of the mortar, and the optimum temperature is 70 °C-80 °C. The maximum compressive strength and flexural strength of mortar can be obtained by continuous curing at high temperature for 4d, while 91.9% of the maximum compressive strength and 71.3% of the maximum flexural strength can be obtained respectively by curing for 24h. The sensitivity factors from large to small on mechanical properties of mortar as follows: water phase content, water glass modulus, the cement/sand ratio and the solution/cement ratio. The strength of mortar decreases sharply with the increase of water content z, and the two have almost linear relationship. The compressive strength and flexural strength of the mortar first increase and then decrease with the increase of the modulus n of the water glass, satisfying the quadratic curve relationship. The effect of cement/sand ratio and solution/cement ratio on the strength of mortar can be ignored. When the porosity is similar, the larger the volume ratio of the gel aperture (≤10nm) and the transition aperture (10nm-100nm), the higher the strength of the mortar. However, the effect of porosity on the strength is significantly greater than the influence of pore size distribution.