Climate change is reshaping the thermal environment of Meriones meridianus habitats in the Mu Us Desert in China. However, the trade-off between behavioral plasticity and physiological adaptations in this species when coping with extreme temperatures across seasons remains poorly understood. Here, we measured activity patterns and serum and brown adipose tissue (BAT) metabolite levels in this rodent during summer and autumn, and analyzed their relationships with microhabitat temperatures. Behaviorally, 87.9% of extra-burrow summer activity occurred between 22:00-01:00, while autumn activity showed a bimodal distribution: 40.9% concentrated during 18:00-20:00 and 18.9% during 03:00-06:00. This temporal niche shifting effectively minimizes direct heat exposure in summer but provides incomplete protection against autumn cold exposure. Physiologically, serum metabolite concentrations exhibited significant seasonal variations. Specifically, metabolites associated with glycolysis, the tricarboxylic acid (TCA) cycle, oxidative phosphorylation, and pathways contributing to acetyl-CoA or TCA cycle intermediates production were downregulated in autumn. Conversely, glycolysis, pyruvate oxidation, the TCA cycle, and oxidative phosphorylation pathways in BAT were significantly enhanced in autumn. Notably, adenosine 5'-triphosphate (ATP) levels in BAT showed no significant seasonal differences. This physiological linkage suggests chronic cold activation of BAT in autumn. Our results show a trade-off where behavioral thermoregulation sufficiently counteracts summer heat through temporal niche shifting but fails to mitigate chronic cold exposure in autumn, necessitating physiological adaptations.