Background Parasites are prevalent in animals and have coexisted with their hosts over long evolutionary periods. However, the link between individual behavioral variations and parasitic infections remains unclear. Plateau pika ( Ochotona curzoniae ) is a keystone species on the Qinghai-Tibetan Plateau that is commonly infected with Eimeria spp., an intestinal parasite. Methods In this study, 30 adult pikas were assigned to three groups: infected with Eimeria spp. (PA+), administered normal saline (Ctrl), and treated with an anticoccidial drug (PA−). We examined changes in boldness, exploration, and docility, as well as variations in triiodothyronine (T3), thyroxine (T4), resting metabolic rate (RMR), and fecal cortisol (CORT) levels. Results The PA+ group exhibited significantly higher parasite load. Pikas showed increased boldness, exploration, and docility on day 5, when Eimeria spp. numbers were high. The T3 and T4 levels declined as parasite loads increased, whereas the CORT and RMR levels fluctuated at different experimental stages. These results suggest that parasite infection influences host behavior and physiology, providing insights into parasite-host interactions. Conclusion This study provides evidence that Eimeria spp. load modulates the behavior and physiology of plateau pikas. The specific behavioral shifts coinciding with peak infection, coupled with the suppression of thyroid hormones and metabolic responses, reveal a complex and integrated host adaptation strategy. As a keystone species on the Qinghai-Tibet Plateau, the behavior-physiology coupling mechanism in plateau pikas not only provides new evidence for host-parasite coevolution, but also offers critical insights into understanding the stability of regional ecosystems.