A phenotypic and gene mutation study was carried out to investigate the molecular mechanism of inherited protein C deficiency in a family with the disorder. The proband was a 21-year-old male who was admitted to hospital due to swelling of the left lower limb for 3 months and hemoptysis with chest tightness for more than 1 week. The clinical diagnosis was pulmonary embolism and deep vein thrombosis of the left lower limb. Plasma protein C activity, protein S activity and antithrombin Ⅲ activity were detected in the patient and their family members. Whole exon sequencing was used to analyze a total of 199 genes associated with thrombus susceptibility of the patient. After the mutation was found and Sanger sequencing was used to verify whether the family members carried the same gene mutations as the patient. The conservation of amino acid mutation sites was analyzed by using the software ClustalX-2.1-win. The damage of mutations to protein function was analyzed by PROVEAN and PolyPhen-2 online bioinformatics software. Finally, PyMOL 2.3 software was used to analyze the protein model. The patient and four family members all had the identical heterozygous missense mutation c.1019 C>T (p. Thr340Met) in exon 9 of the protein C gene, resulting in various degrees of protein C deficiency. The Thr340 amino acid was discovered to be poorly conserved in seven homologous species after investigation with the clustalx-2.1-win software. P. Thr340Met was found to be a detrimental mutation by both PROVEAN and PolyPhen-2 online bioinformatics program. The mutation of Thr340 to Met340 caused the hydrogen bond between Thr340 and Gln226 to dissolve, changing the spatial arrangement of protein C, which might be the main explanation for the lower protein C activity, according to the protein model. Protein C deficiency in this family was caused by a hybrid missense mutation C. 1019 C>T (p. Thr340Met). Protein C deficiency may present in varying severity among mutation carriers at the same locus of the protein C gene. Whole-exome sequencing may be considered in young patients with spontaneous venous thromboembolism, even if there is no relevant family history.