The legal system of parentage is a mature rule in traditional civil law, encompassing the acknowledgment and denial of parent-child relationships. In China, the parentage legal system outlined in the Civil Code is a guiding provision that requires supplementary operational rules. The rule of parentage presumption, as a crucial component of the parentage legal system, serves as the premise and foundation of the entire parentage system. China’s parentage presumption involves both legal and factual presumptions. To elucidate the legislative intent and objective expression of the legal provisions concerning parentage in the Civil Code, it is necessary to clarify the legal attributes, logic, and effects of parentage presumption. Based on this, deviations in legal application due to inconsistent interpretations by different judges should be identified and adjusted. There exist four challenges in the practical application of the parentage presumption rule within the Chinese judicial system. It is imperative for judges to possess a precise and consistent understanding of these challenges. Article 1073 of the Civil Code and judicial interpretations constitute a remedial mechanism for parentage presumption. However, for this article to yield the intended legal effects, detailed specifications are needed regarding the parties eligible to file denial lawsuits of legitimate children, the grounds for denial, and the statute of limitations. Additionally, the implied recognition system reflected in the legal provision should also be supplemented with unified and applicable regulations to ensure operability within China’s legal system. Only with consistent legislative interpretations and applications can the consistency of legal application in parentage relationships be safeguarded, thereby upholding the authority of the Civil Code.