The penetration of smartphones into human life finds expression in problematic smartphone use, particularly under the Covid-19 home confinement. Problematic smartphone use is accompanied by adverse impacts on personal wellbeing and individual performance. However, little is known about the mechanism of such adverse impacts. Motivated by this, the present study strives to answer (i) how bedtime smartphone use impacts students’ academic performance through wellbeing-related strains; (ii) how to mitigate the adverse consequences of bedtime smartphone use. Drawing upon the stressor-strain-outcome paradigm, the current work presents a comprehensive understanding of how smartphone use indirectly deteriorates college students’ academic performance through the mediators of nomophobia — “the fear of being unavailable to mobile phones” (Lin et al., 2021) — and sleep deprivation. This allows a more flexible remedy to alleviate the adverse consequences of smartphone use instead of simply limiting using smartphones. This study collects a two-year longitudinal dataset of 6093 college students and employs the structural equation modeling technique to examine the stressor‐strain‐outcome relationship among bedtime smartphone use, nomophobia, sleep deprivation, and academic performance. This study finds robust evidence that wellbeing-related strains (i.e., nomophobia and sleep deprivation) mediate the negative relationship between bedtime smartphone use and academic performance. Furthermore, engaging in physical activity effectively mitigates the adverse effects of bedtime smartphone use upon nomophobia and sleep deprivation. This study not only enriches the current literature regarding the indirect effect mechanism of smartphone use but also provides valuable insights for academics and educational policymakers.