Electron transports in the α-domain and β-domain of proteins have been comprehensively investigated. The structure-dependent electron transport of proteins has been experimentally measured and theoretically simulated, and both the theoretical and experimental results demonstrate significant differences in electrical conductivity between the α-domain and β-domain. By controlling the feedback system of the scanning tunneling microscope (STM), the conductance of a single α-domain protein hemoglobin (Hgb) and a β-domain protein superoxide dismutase enzyme (SOD) were measured, respectively. The current signal of Hgb is obviously stronger, indicating that the α-domain is more conductive. To confirm our finding, molecular orbitals of both the β-domain in SOD and α-domain in Hgb have been analyzed based on first-principles calculations. As expected, tunneling transport and hopping in the α-domain are both more efficient, indicating that it is easier for electrons to transport through the α-domain, which are in great agreement with our experimental data. In order to explain our results, molecular structures of α- and β-domains have been carefully analyzed and show that the explanation should lie in the differences in packing mode between the α-domain and β-domain. This research should be very important to application prospects in molecular electronics.