The　estimation　methods　of　reproduction　numbers　and　serial　intervals　are　important　in　the　early　stages　of　infectious　diseases.　During　the　COVID　pandemic,　China　implemented　a　dynamic　zero-COVID　policy　on　the　Chinese　mainland　until　the　end　of　2022.　This　study　compares　three　estimation　methods　of　basic　reproduction　numbers　on　small-scale,　short-duration　COVID-19　epidemics　in　Fujian　Province.　Basic　reproduction　numbers　were　investigated　using　a　varying-strain　model　via　a　next-generation　matrix　method.　Serial　intervals　were　derived　using　the　infector–infectee　pairs　of　two　epidemics　from　the　Fujian　Provincial　Center　for　Disease　Control　and　Prevention.　Basic　reproduction　numbers　were　estimated　using　the　maximum　likelihood　estimation　method　and　the　exponential　growth　method.　The　curves　of　the　effective　reproduction　numbers　of　the　three　epidemics　were　plotted　by　utilizing　daily　cases　and　the　EpiEstim　R　package.　The　spatial　heterogeneity　of　infection　cases　was　described　using　the　Gini　coefficient.　This　study　provides　significant　insights　on　the　estimation　methods　of　reproduction　numbers　for　policymakers　in　the　local　government.　The　results　reveal　that　social　contacts　between　infectors　and　susceptible　individuals　should　be　reduced　to　avoid　an　increase　in　deaths　and　to　fight　against　the　spread　of　infectious　diseases.　©　2024