<p>The coronavirus disease 2019 (COVID-19) pandemic has significantly affected global public health since its emergence in late 2019. This study aimed to investigate the temporal and spatial dynamics of SARS-CoV-2 transmission in South Korea from 2020 to 2022, with particular emphasis on the effects of changes in quarantine policy and viral lineage evolution. Using 77,224 high-quality whole-genome sequences, phylogenetic analyses were performed to evaluate lineage introductions, substitution rates, and cryptic transmission patterns across distinct phases of the pandemic. Additionally, Bayesian phylogeographic analyses were conducted to reconstruct transmission patterns within South Korea. The findings revealed a substantial increase in the number of monophyletic clusters following the relaxation of quarantine measures, particularly during the period of Omicron sub-lineage predominance. Phylogeographic reconstructions identified Seoul and Gyeonggi Province as major transmission hubs nationwide. Substitution rate analyses indicated a progressive decline over time, with Omicron sub-lineages exhibiting significantly reduced evolutionary rates compared to earlier variants. A novel recombinant variant was detected; however, it did not result in sustained transmission. These findings provide indirect evidence that non-pharmaceutical interventions were effective in limiting the introduction and spread of novel viruses, although they could not completely prevent outbreaks. The adaptation and strengthening of such control strategies should be considered in preparing for next pandemics.</p>