Plateau pika (Ochotona curzoniae, hereafter pika) is an ecosystem engineer on the Qinghai-Tibetan Plateau (QTP), whose activity exerts a profound effect on the ecosystem nutrient cycle of alpine grasslands. However, the quantification of pika activity effects on ecosystem carbon (C) and nitrogen (N) stocks remains limited. Based on aerial photography and field surveys conducted in 19 sites of alpine grasslands in 2018, 2020 and 2023, we first investigated the interannual variation of pika density and the area of underlying surfaces (original vegetation, pika mounds and bare patch), and subsequently quantified the effect of pika activity on ecosystem C and N stocks. Pika density first increased and subsequently decreased during 2018–2023. Their population density ranged from 6.85 to 44.65 per hectare for all grasslands, belonging to the moderate level. The area of original vegetation increased but that of bare patch decreased from 2018 to 2023 for most grasslands. Both new and old pika mounds showed small interannual variation and their area fractions were less than 1.2 % for all grasslands. Pika foraging, burrowing and eroded pika mounds primarily affected the ecosystem C and N stocks. Under the current pika density, their activity caused approximately 0.12–0.28 % and 0.08–0.20 % reductions of ecosystem C and N stocks. Our results suggested that pika activity had a minor effect on ecosystem C and N stocks under moderate density, and this effect was highly dependent on the intensity of their activity. Given the engineering and keystone roles of pika on the QTP, we strongly recommend that policy-makers and regulatory agencies to regulate pika density within a reasonable range instead of advocating for eradication.