Infrastructure constructions in highly mountainous areas (especially in Qinghai-Tibet Plateau with an average altitude close to 5000 m) are developed rapidly in recent years. Meanwhile, the lower atmospheric pressure effects caused by higher altitude on building material have to be carefully evaluated. In this study, the microstructure characterization during hydration behavior of Portland cement under applied low atmospheric pressures, i.e., 0.2, 0.5, 0.8, 0.9 times of 1.0 atmospheric pressure (P0), was experimentally investigated using X-Ray diffraction (XRD), thermogravimetric analysis (TGA), and low temperature nitrogen adsorption techniques, in which the degree of hydration (DoH), the evolution of hydrates, and pore size distribution were assessed. Experimental results revealed that lower curing pressures had diminishing effects on the DoH, especially less than seven days. Although XRD cannot quantitatively identify the hydrate phases under lower curing pressures, TGA analysis provided evidences that both portlandite, ettringite, and calcium silica hydrate (CSH) phases decreased with reduced curing pressures from P0 to 0.2P0. Lower curing pressures caused increased cumulative volumes in micropores and mesopores, but have marginal effects on macropores based on nitrogen absorption evaluation on pore size distribution at 28 days of hydration. Moisture evaporation due to the lower curing pressure was confirmed by TGA measurement. The experimental results under lower curing pressures were served as inputs for thermodynamic simulation to predict hydrated products which confirmed the experiment data and indicated that the lower curing pressure caused more capillary pores in cement pastes. There were three concerns including DoH effect, w/c effect, and moisture evaporation effect that were considered as main reasons influencing the microstructures of cement paste cured under lower pressures.