The low atmosphere-pressure in plateau regions will affect the bubble stability, thus affecting the air-void structure and frost resistance of air-entrained concrete. The effect of atmosphere pressure on the pore structure of freshly mixed air-entraining mortar was investigated via constructing a self-built low atmosphere pressure mixing device. The results show that the decrease of atmosphere pressure can decrease the initial air content of air-entrained mortar, increase the bubble spacing coefficient as well as air content loss through time, and deteriorate the pore structure. The mechanism of low atmosphere pressure effect on the pore structure of air-entrained mortar is mainly since the reduced atmosphere pressure accelerates the Ostwald ripening process of the bubble system, which makes the small bubbles smaller until they disappear and the large bubbles larger until they break, and the average pore size of the bubble system increases, thus accelerating the destabilization rate of the bubble system. These findings have important implications for understanding the mechanism of bubble destabilization under a low atmosphere pressure and developing the corresponding bubble stabilization techniques.