As one of the dominant species of the alpine grassland on the Qinghai–Tibet Plateau, the activities (e.g., gnawing, burrowing, and grass storage) of plateau pikas (Ochotona curzoniae) directly alter the plant community structure of the grassland ecosystem and affect livestock production and greenhouse gas emission. In order to investigate the effects of rodent isolation (RI) on plant community structure and greenhouse gas emission in the alpine grassland of the Qinghai–Tibet Plateau, we established plots of rodent isolation and rodent activity (i.e., the control sample (CK)) in the 14th village, Seni District, Nagqu City in May 2018. From July 2019 to September, the numbers, sizes, and total damaged area of effective holes; the height, coverage, and aboveground plant biomass; and the methane (CH₄) and nitrous oxide (N₂O) emissions of the alpine grassland were monitored by the quadrat survey method and static closed-chamber method. The results show that the invasion and tunneling of Ochotona curzoniae resulted in the destruction of alpine grassland measuring 0.064 m² per square meter, while the rodent isolation plots showed that 97.9% of the alpine grassland remained unaltered; such unaffected land implies that the economic income of herdsmen could increase by 140 CNY hm⁻². The rodent isolation plots also show that the height and proportion of grasses and sedges in the alpine grassland increased, while the proportion of poisonous weeds decreased. Moreover, the rodent isolation plots also showed a significantly increased coverage of aboveground biomass (p < 0.05), although species richness showed no significant effect based on the Shannon–Weiner, Simpson, and Pielou indices (p > 0.05). The soil uptake of CH₄ and N₂O was 204.99 ± 50.23 μg m⁻² h⁻¹ and 4.48 ± 1.02 μg m⁻² h⁻¹ in the rodent isolation plots, significantly higher by 465.75% and 3001.4% relative to the rodent activity plots, respectively (p < 0.05). Therefore, the establishment of rodent isolation areas can effectively alleviate the degree of damage to alpine grasslands in the short run and slow down the greenhouse gas emission rate to some extent. However, excessive rodent control may also have negative effects on grassland ecosystems, so more attention should be paid in future studies to determining the disturbance threshold of plateau pika in this area. These results provide theoretical guidance for rodent control, grassland protection, and ecological environment management on the Qinghai–Tibet Plateau.

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