Perhaps because Yushan is located in the most remote part of Taiwan's mountainous regions, and access is difficult, it has largely escaped deforestation, with the exception of the cypress forests of the Nantsaihsien River, which were completely logged out, and outlying areas such as Tungpu and Tataka. The core areas in the center of the national park still boast virgin forests and a vibrant ecology.
或許是玉山位居台灣山區最深處，交通實在不便，近代的森林浩劫除了使楠梓仙溪的檜木林砍伐殆盡，並波及東埔、塔塔加等外圍地區，園區中央的核心地帶仍有大片原始林，生態樣貌豐富。