The invention discloses polymer cement-based modified mortar. The polymer cement-based modified mortar comprises the following raw materials in parts by mass: 200 to 350 parts of fine sand, 80 to 140parts of cement, 20 to 30 parts of ceramic powder, 15 to 25 parts of clay, 10 to 30 parts of rubber powder, 5 to 15 parts of diatomite, 5 to 15 parts of graphite powder, 8 to 20 parts of polymer emulsion, 5 to 10 parts of basalt fiber, 3 to 8 parts of polyacrylonitrile fiber, 2 to 5 parts of a water-reducing agent, 1 to 3 parts of a defoaming agent, 2 to 5 parts of a coupling agent and 50 to 150 parts of water. The polymer cement-based modified mortar has advantages of high structural strength, high waterproofness, high toughness, high bending strength, high volume stability, high durability,high freezing resistance, high early strength and good use effect, and is not liable to crack.