Familial hypercholesterolemia (FH) is a severe genetic hyperlipidemia characterized by increased levels of low-density lipoprotein cholesterol (LDL-C), leading to premature atherosclerosis. Angiopoietin-like protein (ANGPTL3) is a hepatocyte-specific protein that can be used to lower LDL in FH. However, it was unknown whether ANGPTL3 variants are present in FH patients. This study was performed to identify ANGPTL3 variants in unrelated Chinese Han patients with FH. We screened 80 patients with FH (total cholesterol >7.8mmol/L, LDL-cholesterol >4.9mmol/L) and 77 controls using targeted next-generation sequencing (NGS) of six FH candidate genes (LDLR, ApoB100, PCSK9, ABCG5, ABCG8, and ANGPTL3). Candidate pathogenic variants identified by NGS were validated by Sanger sequencing. Mutant and wild-type plasmids containing the variant sequence were constructed and verified by Sanger sequencing. The gene expression profile was analyzed by an expression profile chip in transfected HepG2 cells using quantitative real-time (qRT)-PCR. We identified 41 variants in 28 FH patients, including two ANGPTL3 mutations: one exonic (c.A956G: p.K319R) and one in the untranslated region (c.*249G>A). Gene ontology analyses found that the cholesterol metabolic process and ANGPTL3 expression were significantly up-regulated in the ANGPTL3 K319R mutation group compared with the wild-type group. qRT-PCR findings were consistent with the expression profile analysis. Rare ANGPTL3 variants were identified in Chinese patients with FH, including ANGPTL3: p.(Lys319Arg) which affected the expression of ANGPTL3 and the cholesterol metabolic process as determined by bioinformatics analysis. Chinese Clinical Trial Registration (ChiCTR-ROC-17011027) http://www.chictr.org.cn/listbycreater.aspx.