Background Glycogen storage disease (GSD) is a relatively rare inborn metabolic disorder, our study aims to investigate the genotypic and clinical feature of hepatic GSDs in China. Methods The clinical and genotypic data of 49 patients with hepatic GSDs were collected retrospectively and analyzed. Results After gene sequencing, 49 patients were diagnosed as GSDs, including GSD Ia (24 cases), GSD IIIa (11 cases), GSD IXa (8 cases), GSD VI (3 cases) and GSD Ib (3 cases). About 45 gene variants ofG6PC,AGL,PHKA2,PYGL, andSLC37A4were detected; among which, 22 variants were unreported previously. c.648G>T (p. Leu216Leu) ofG6PCexon 5 is the most common variant for GSD Ia patients (20/24,83.33%?, splice variant c.1735+1G>T ofAGLexon 13 is relatively common among GSD IIIa, while novel variant accounts for the majority of GSD IXa and GSD VI patients. As for clinical features, there was no significant difference in the onset age among group GSD Ia, GSD IIIa, and GSD IXa, but the age at diagnosis and average disease duration from diagnosis of GSD Ia were significantly higher than GSD IIIa and GSD IXa. Body weight of GSD patients was basically normal, but growth retardation was relatively common among them, especially for GSD Ia patients; and renomegaly was only found in GSD Ia. Besides, serum cholesterol, triglyceride, lactic acid, and uric acid in GSD Ia were significantly higher than those with GSD IIIa and IXa (p < 0.05); but ALT, AST, CK, and LDH of GSD III and GSD IXa were significantly higher when compared to GSD Ia (p < 0.05). Conclusions All hepatic GSDs patients share similarity in clinical and biochemical spectrum, but delayed diagnosis and biochemical metabolic abnormalities were common in GSD Ia. For family with GSD proband, pedigree analysis and genetic testing is strongly recommended.