Hustai National Park has a diverse range of flora, and although the park is classified as a mountain steppe region, varied floral communities can be identified. These include sand dunes, shrubs, steppe, meadows, tussock grasslands and woodlands in the mountain steppe region and riverine forests and aquatic communities in the Tuul River valley. Floral diversity has evolved as a result of the area's varied microclimates.

The park's landscape is dominated by a central mountain range of granite rock, a southwestern spur of the Khentii range that runs from southwest to northeast. To the north, the mountain range slopes down to a rolling plain with fields of cereal crops, while to the south, it borders the broad valley of the meandering Tuul River. The rounded peaks feature spectacular rocky outcrops carved by the wind and frost, and small caves hidden in the granite. The southern mountainsides tend to feature more exposed rock as the slopes receive more sunlight and less rain, inhibiting plant growth and accelerating erosion. Erosion caused by heavy summer downpours and melting spring snow have led to the formation of gullies and the accumulation of thick layers of eroded material in the valleys.

The most northern part of Hustai is a small area of sand dunes 5km outside the border of the park, but which is included under the protected area. The dunes are thought to be the remains of a lake which dried up thousands of years ago, having been moulded by the wind from what was once the lake bottom.

Steppe vegetation together with shrubland dominate 90% of the approximately 50,000-ha. park. Small patches of forest cover about 5% of the park area and consist mainly of birch woodlands (Betula platyphylla) and poplars (Populus tremula). Together with Siberian needlegrass (Festuca sibirica) they are scattered intermittently across northern slopes exceeding 1,400m.

About 450 vascular plant species can be found in Hustai National Park. Among these are several endemic, rare or Red Book species such as Juniperus sabina. Throughout the year the composition and appearance of vegetation changes. During warmer months, Eidelweiss grow in sufficient density so that nomadic families can use their soft flower heads to fill pillows and produce match sticks from their stalks. In spring, many slopes turn pink or purple with a bloom of Amygdalus shrubs and Pulsatilla. On hot summer days, the air is filled with etheric oils from Artemisia and wild thyme. In autumn, the deciduous forests and shrub communities transform the park into a palette of red, orange and yellow. Most valleys contain many wildflowers for the majority of the growing season.

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