The Karakoram-Himalaya region is a vital part of the Pan Third Pole area. In this paper, we studied the spatial patterns and characteristics of the ecoregions and protected areas in the Karakoram-Himalaya region, which is the transboundary area of China, Afghanistan, Pakistan, India, Nepal, Bhutan, and Myanmar. We found that the Karakoram-Himalaya region spanned Palearctic and Indo-Malayan biogeographic realms with a total area 902843.76 km². It covers 14 ecoregions and 55 protected areas are included. The protected areas are composed of the national parks and nature reserves, which are mainly distributed in the eastern Himalayan subalpine conifer forests, Himalayan subtropical broadleaf forests, and eastern Himalayan broadleaf forests. The total area of the protected areas is 159063.30 km² accounting for 17.62% of the Karakoram-Himalaya region. There are 41 national parks that account for 74.50% of the number of the protected areas; 25 protected areas are adjacent to more than two countries and account for 45.45%. The geographical concentration indexes of the protected areas are all above the completely average value of 37.796, which means the spatial distribution is concentrated. Among which the distribution of nature reserves is more maldistribution than the national parks, mainly distribute in China, Nepal, and India. The kernel density estimation showed that the protected areas were highly grouping in the transboundary of China-Nepal and China-India. Since the 1930s, more and more countries in this region have established protected areas especially since the 1980s, and now they have formed the most noted protection aggregation stripe. This paper is significant to the research of transboundary cooperation between the national parks in the Karakoram-Himalaya region in the future.