The rapid spread and remarkable mutations of SARS‐CoV‐2 variants, particularly Omicron, necessitate an understanding of their evolutionary characteristics. In this study, we analyzed representative high‐quality whole‐genome sequences of 2008 SARS‐CoV‐2 variants to explore long‐term dynamic changes in genomic base (especially GC) content and variations during viral evolution. Our results demonstrated a highly negative correlation between GC content and variant emergence time (r = −0.765, p < 2.22e−16). Major gene partitions (S, N, ORF1ab) displayed similar trends. Omicron exhibited a significantly lower GC content than non‐Omicron variants (p < 2.22e−16). Notably, we observed a robust negative correlation between C and T content (r = −0.778, p < 2.22e−16) and between G and A content (r = −0.773, p < 2.22e−16). Among all strains, Omicron showed the greatest base variation, with C‐>T mutations being the most frequent (median interquartile range IQR: 29 (27, 31), 37.67%), succeeded by G‐>A mutations (11 (9, 13), 14.63%). Over a 3‐year span, an annual decline rate of 0.12% in SARS‐CoV‐2 GC content was observed and could become more pronounced in future emerging variants. These findings provided insights into the evolutionary trajectory of SARS‐CoV‐2, underscoring the significance of continuous genomic surveillance for effective prediction of and response to future variants.