Climatic conditions in plateau areas can enormously affect the properties and microstructure of cement-based materials. This research investigates the strength development and microstructural changes in magnesium phosphate cement (MPC) mortars in a plateau environment. Experiments were conducted in parallel in a plateau area (Lhasa) and a plain area (Chengdu) to evaluate the effects of the water-to-binder ratio (w/b = 0.12, 0.14 and 0.16) and sand-to-binder ratio (s/b = 0.5, 0.75 and 1) on the compressive and flexural strength of MPC mortars. At the same time, hydration products were characterized via XRD, TGA, and SEM/EDX micro-analyses, and the porosity of the materials was also analyzed via MIP. The results demonstrated that curing in a plateau environment resulted in a decrease in workability and yielded higher strength at an early age (before 1 day) but degraded the long-term (180-day) strength of MPC mortars when compared with curing in a plain environment, irrespective of w/b and s/b ratios. Unlike the plain group, the plateau group revealed the deterioration of microstructures over time, including the decrease in struvite content, the morphology change in struvite crystals, and the increase in porosity, which resulted in the degradation of mechanical properties between 1 and 180 days. The strength loss can be effectively alleviated at lower w/b and s/b ratios.