Mountain area accounts for a high proportion of the land area in China, and it is the focal area to solve the contradiction of imbalanced regional development, as well as an important source of ecosystem services. Therefore, this area has been facing long-term pressure and challenges in economic development and ecological protection. In this paper, we selected a rocky desertification mountain area, an active mountain area of new tectonic movement and a typical northern earth-rock mountain area, as Qian-Gui karst Mountain area, Hengduan Mountain area and Taihang Mountain area, as examples to represent three main types of mountain areas. Three representative types of ecosystem services, including NPP (Net Primary Productivity) as a support service, water conservation as a regulation service, and agricultural produce as a supply service, were incorporated into this study. Linear regression, correlation analysis and other methods were then used to investigate the spatial-temporal characteristics of the trade-offs and synergies in each of the three kinds of mountain areas during 1990-2015 in China. The analysis yielded three main conclusions for the three mountainous areas. (1) The agricultural produce supply service decreased relatively, while the support and regulation services of NPP and hydrological regulation increased significantly. (2) There was a synergistic relationship between NPP and the hydrological regulation services in the three mountainous areas. The synergistic relation in Qian-Gui karst Mountain area became enhanced, while those in Hengduan and Taihang Mountain areas became weakened, and the former was weakened to a greater extent. There was a trade-off between NPP, the hydrological regulation service and the agricultural produce supply service among the three mountainous areas. In particular, the trade-off between NPP and the agricultural produce supply service in Qian-Gui karst Mountain area became weaker, while those in Hengduan and Taihang Mountain areas were enhanced, and the latter was enhanced to a greater degree. (3) Significant spatial differentiation was evident in the trade-offs and synergies of ecosystem services among the three mountain areas.