The Tianshan Mountain area is a large system of mountain ranges that spans China and a number of other Central Asian countries, with a length of more than 1700 km within the Xinjiang Uyghur Autonomous Region, northwest China. It has a typical temperate continental climate, has abundant forest and grassland resources, and is one of the most important water sources in the arid region of Central Asia. The Tianshan Mountains are also considered a biodiversity hotspot that plays a key role in the function of regional ecosystems, providing various habitats for plants and animals, including butterflies, which are considered environmentally sensitive and thus have potential to be used as ecological indicators. Surveys in the Xinjiang eastern Tianshan Mountains from 2006 to 2008 recorded 63 species of butterflies, which belonged to seven families and 43 genera, accounting for 24.80% of the total butterfly species recorded in Xinjiang. Palearctic species were dominant (73%), while widely distributed species made up the rest of the species (27%). No oriental species were recorded because of the geographical isolation. The Nymphalidae were the most diverse group with 19 species and 11 genera, while only 1 species of Riodinidae was recorded. The butterfly habitats in the Xinjiang eastern Tianshan Mountain area were divided into 5 altitudinal zones, including low mountain shrub grassland, mountain forest steppe, subalpine meadow, alpine meadow, and the cushion vegetation zone. In terms of butterfly species richness and total butterfly abundance these habitat zones were ranked from highest to lowest as follows: subalpine meadow > mountain forest steppe > low mountain shrub grassland > alpine meadow > cushion vegetation zone. The diversity of butterfly species, genera, and families were comprehensively evaluated using the Shannon-Wiener index and the G-F index. The results indicated that subalpine meadow habitats had the highest species diversity, followed by mountain forest steppe, low mountain shrub grassland, alpine meadow habitats, and finally the cushion vegetation zone. The Shannon and G-F indices showed similar patterns, demonstrating high species evenness among habitats and similar distribution patterns of butterfly families, genera, and species diversity in the study area. Changes in the number of species and butterfly abundance were related to changes in altitude, initially increasing with altitude and then declining. The fauna composition also changed along the altitudinal gradient. The proportion of widely distributed species gradually declined, and there was no distribution especially in meadow and cushion vegetation zone. However, Palearctic species showed an opposite trend, rising with increasing altitude. Our results indicate that butterfly communities in the eastern Tianshan Mountain area were different from those at Altai Mountain and two other parts of the Tianshan Mountain area. Both diversity and fauna composition were strongly affected by different types of habitats. Attention should be paid to the potential consequences of habitat loss on butterflies that are only distributed in the cushion vegetation and alpine meadow zones. These species and habitats are particularly vulnerable as temperatures are expected to rise by a greater amount at higher altitudes in the future, which could cause the snowline to rise. To avoid the irreversible loss of biodiversity, habitat protection should be considered fundamental for the conservation of butterflies, and particularly the preservation of higher altitude habitats.