There　is　an　increasing　demand　for　prenatal　paternity　testing　in　the　forensic　applications,　which　identify　biological　fathers　before　the　birth　of　children.　Currently,　one　of　the　most　effective　and　safe　Non-Invasive　Prenatal　Paternity　Testing　(NIPPT)　methods　is　high-throughput　Next-Generation　Sequencing　(NGS)-based　SNP　genotyping　of　cell-free　DNA　in　maternal　peripheral　blood.　To　the　best　of　our　knowledge,　nearly　all　methods　being　used　in　such　applications　are　based　on　traditional　postnatal　paternity　tests　and/or　statistical　models　of　conventional　polymorphism　sites.　These　methods　have　shown　unsatisfactory　performance　due　to　the　uncertainty　of　fetal　genotype.　In　this　study,　we　propose　a　cutting-edge　methodology　called　the　Prenatal　paternity　Test　Analysis　System　(PTAS)　for　cell-free　fetal　DNA-based　NIPPT　using　NGS-based　SNP　genotyping.　With　the　implementation　of　our　proposed　PTAS　methodology,　63　out　of　64　early-pregnancy　(i.e.,　less　than　seven　weeks)　samples　can　be　precisely　identified　to　determine　paternity,　except　for　one　sample　that　does　not　meet　quality　control　requirements.　Although　the　fetal　fraction　of　the　non-identified　sample　is　extremely　low　(0.51%),　its　paternity　can　still　be　detected　by　our　proposed　PTAS　methodology　through　unique　molecular　identifier　tagging.　Paternity　of　the　total　313　samples　for　mid-to-late　pregnancy　(i.e.,　more　than　seven　weeks)　can　be　accurately　identified.　Extensive　experiments　indicate　that　our　methodology　makes　a　significant　breakthrough　in　the　NIPPT　theory　and　will　bring　substantial　benefits　to　forensic　applications.　©　2023　The　Authors