Depicting a taxonomic group's evolutionary trajectory as a function of changes in the geographical landscape and its historical distribution is critical for constructing informed conservation strategies. Based on fossil sites from the Pliocene to the Holocene, and historical records since 1175 AD, we established macaques’ dispersal pathways into and through China. These routes include internal pathways starting from the southeast corner of the Qinghai-Tibet Plateau and Mts. Hengduan in western China, and the routes through the estuaries of the three major rivers (Yangtze, Yellow, and Pearl). Our results indicate that macaques used the three rivers and avoided the higher elevation of the plateaus to promote their radiation. They occupied the whole mainland and islands in the Pleistocene and experienced shrunken distribution in the Holocene due to climate changes and human-induced activities. A prominent China-wide reduction occurred between 1817 and 1917; and a remarkable retraction from central China happened between 1918 and 2018 following further eco-social development and human expansion in central China, particularly since the second half of the last century. Starting in 1175 there was a restriction of range to higher altitudes, so that macaques have contracted their range to the west, and the Qinghai-Tibet Plateau and Mts. Hengduan have become an important sanctuary. We predict that if the current climate and human-induced changes are not reversed by decisive conservation actions, macaques in east and central China will likely be extinct in the near future.