The COVID-19 pandemic has become a world-wide health crisis. So far, most studies have focused on the epidemiology and pathogenesis of this infectious disease. Little attention has been paid to the disease sequelae in patients recovering from COVID-19, and nothing is known about the mechanisms underlying these sequelae. Herein, we profiled the serum proteome of a cohort of COVID-19 patients in the disease onset and recovery stages. Based on close integration of our proteomic analysis with clinical data, we propose that COVID-19 is associated with prolonged disorders in cholesterol metabolism and myocardium, even in the recovery stage. We identify potential biomarkers for these disorders. Moreover, severely affected patients presented more serious disturbances of these pathways. Our findings potentially support clinical decision-making to improve the prognosis and treatment of patients.