The invention provides polymer mortar and a preparation method thereof. The polymer mortar comprises the following raw material components in parts by weight: 90-100 parts of rapid hardening sulphoaluminate cement, 35-45 parts of a polymer emulsion, 2-3 parts of superfine powder, 5-10 parts of gypsum powder, 5-10 parts of an expanding agent, 190-210 parts of sand, 30-40 parts of water, 0.5-1.0 part of a powder water reducing agent, 0.5-1.0 part of polymer fiber, 0-0.05 part of a hardening accelerator, 0-0.05 part of a retarder and 0.3-0.8 part of a defoaming agent. The method comprises the following steps: preparing a dry powder material, preparing a pre-dispersed emulsion, adding the dry powder material, the pre-dispersed emulsion, the water and the defoaming agent into a stirrer, and mixing and stirring for 1-3 minutes to a uniform state, thereby obtaining the polymer mortar. The polymer mortar can meet the construction requirements of the filling layer of a CRTS II type slab ballastless track.