Cuc Phuong National Park lies at the south-eastern extent of a limestone range that runs north-west to Son La province. This limestone range predominantly comprises karst, marine in origin and perhaps 200 million years old. The section of the limestone range encompassed by the national park rises sharply out of the surrounding plain, to elevations of up to 636 m. This section is around 10 km wide and 25 km long, and has a central valley running along almost the entire length.
The karst topography exerts a dominant influence on drainage patterns in Cuc Phuong. Most of the water that the national park receives is quickly absorbed by a complex underground drainage system common to mature karst landscapes, often emerging from springs on the lower slopes flanking the national park. For this reason, there are no natural ponds or other standing bodies of water within the national park, and there is only one permanent watercourse, the Buoi river. This river bisects the western end of the national park from north to south, and feeds the Ma river, the major river in Thanh Hoa province.

Biodiversity values
The vegetation of Cuc Phuong National Park is dominated by limestone forest. In some places, the forest is stratified into as many as five layers, including an emergent layer up to 40 m in height. Due to the steep topography, however, the canopy is often broken and stratification is unclear. Many individual trees show well developed buttress roots in response to the generally shallow soils. The national park contains particularly large specimens of certain tree species, including Terminalia myriocarpa, Shorea sinensis, and Tetrameles nudiflora, which have been developed as tourist attractions. There is an abundance of timber trees and medicinal plants.

Cuc Phuong National Park has an extremely rich flora. To date, 1,980 vascular plant species in 887 genera and 221 families have been recorded at the national park. In terms of number of species, the best-represented families in the flora of Cuc Phuong are the Euphorbiaceae, Poaceae, Fabaceae, Rubiaceae, Asteraceae, Moraceae, Lauraceae, Cyperaceae, Orchidaceae and Acanthaceae. The flora of Cuc Phuong contains elements of the Sino-Himalayan, Indo-Burmese and Malesian floras. The high known floral diversity at Cuc Phuong can, however, be partly attributed to the high level of survey effort directed at the site.

Floral surveys have identified three vascular plant species known, to date, only from Cuc Phuong: Pistacia cucphuongensis, Melastoma trungii and Heritiera cucphuongensis. Cuc Phuong National Park is also considered to be one of seven globally significant Centres of Plant Diversity in Vietnam.
Cuc Phuong supports populations of several mammal species of conservation importance, including the globally critically endangered Delacour's Leaf Monkey Trachypithecus delacouri and the globally vulnerable Owston's Civet Hemigalus owstoni. In addition, the nationally threatened Leopard Panthera pardus has been recently recorded at the national park. Furthermore, over 40 bat species have been recorded at the national park, including 17 species from a single cave. Unfortunately, several large mammal species, including Tiger Panthera tigris and White-cheeked Crested Gibbon Hylobates leucogenys, are believed to have become extinct at Cuc Phuong in recent times, mainly due to high hunting pressure and the relatively small size of the national park.