Glypican-3 (GPC3) is a serum marker for hepatocellular carcinoma (HCC) and has excellent specificity and sensitivity. Herein, the construction of an electrochemical aptasensor based on reduced graphene oxide-carboxymethyl chitosan-hemin-palladium nanoparticles (RGO-CMCS-Hemin/Pd NPs) and GPC3 aptamer (GPC3apt) has the function of GPC3 identification and analysis. RGO-CMCS-Hemin/Pd NPs has excellent biocompatibility, large specific surface area and good electrical conductivity, which is not only used as advanced sensing materials to modify the electrode surface to reduce the resistance and increase the signal amplitude, but also used as an electroactive substance to provide electrical signals. GPC3apt as a biometric element makes the aptasensor has good specificity and sensitivity. The GPC3apt can combine with GPC3 and form GPC3-aptamer conjugation, which increases the electron transfer impedance and changes the electrical signal. Under the optimum conditions, the aptasensor had a good linear relationship with the GPC3 concentration in the range of 1.0–100.0 ng ml−1 with R2 of 0.9573. The lower limit of detection was 1.0 ng ml−1. When the aptasensor was applied to GPC3 detection in human serum samples, the recovery was 93.73%–118.83%. In addition, the GPC3 aptasensor has excellent specificity, reproducibility and stability, which is anticipated to be applied for the clinical detection of GPC3.