Introduction:　Regular　and　rapid　large-scale　screening　for　pathogens　is　crucial　for　controlling　pandemics　like　Coronavirus　Disease　2019　(COVID-19).　In　this　study,　we　present　the　development　of　a　digital　point-of-care　testing　(POCT)　system　utilizing　microfluidic　paper-based　analytical　devices　(μPADs)　for　the　detection　of　SARS-CoV-2　gene　fragments.　The　system　incorporates　temperature　tuning　and　fluorescent　detection　components,　along　with　intelligent　and　autonomous　image　acquisition　and　self-recognition　programs.　Methods:　The　developed　POCT　system　is　based　on　the　nucleic　acid　amplification　test　(NAAT),　a　well-established　molecular　biology　technique　for　detecting　and　amplifying　nucleic　acids.　We　successfully　detected　artificially　synthesized　SARS-CoV-2　gene　fragments,　namely　ORF1ab　gene,　N　gene,　and　E　gene,　with　minimal　reagent　consumption　of　only　2.2μL　per　readout,　representing　a　mere　11%　of　the　requirements　of　conventional　in-tube　methods.　The　power　dissipation　of　the　system　was　low,　at　6.4W.　Results:　Our　testing　results　demonstrated　that　the　proposed　approach　achieved　a　limit　of　detection　of　1000　copies/mL,　which　is　equivalent　to　detecting　1　copy　or　a　single　RNA　template　per　reaction.　By　employing　standard　curve　analysis,　the　quantity　of　the　target　templates　can　be　accurately　determined.　Conclusion:　The　developed　digital　POCT　system　shows　great　promise　for　rapid　and　reliable　detection　of　SARS-CoV-2　gene　fragments,　offering　a　cost-effective　and　efficient　solution　for　controlling　pandemics.　Its　compatibility　with　other　diagnostic　techniques　and　low　reagent　consumption　make　it　a　viable　option　to　enhance　healthcare　in　resource-limited　areas.　Copyright　©　2023　Dong,　Mo,　Yu,　Xie,　Zheng　and　Jia.