The human gut microbiome varies substantially across individuals and populations and differentially tames our immunity at steady‐state. Hence, we hypothesize that the large heterogeneity of gut microbiomes at steady‐state may shape our baseline immunity differentially, and then mediate discrepant immune responses and symptoms when one encounters a viral infection, such as SARS‐CoV‐2 infection. To validate this hypothesis, we conducted an exploratory, longitudinal microbiome‐COVID‐19 study involving homogenous young participants from two geographically different regions in China. Subjects were recruited and sampled of fecal specimens before the 3‐week surge window of COVID‐19 (between December 11 and December 31, 2022) in China, and then were followed up for assessment of COVID‐19 and post‐COVID‐19 manifestations. Our data showed that the baseline gut microbiome composition was intricately associated with different COVID‐19 manifestations, particularly gastrointestinal involvement and post‐COVID‐19 lingering symptoms, in both an individual‐ and population‐dependent manner. Our study intriguingly for the first time highlight that the gut microbiome at steady‐state may prepare us differentially for weathering a respiratory viral infection.