In this work, an in situ growth protocol is introduced to fabricate three-dimensional graphene films (3D GFs) on gold substrates, which are successfully utilized as working electrode for electrochemical detection of nucleic acid (microRNA) and protein (lysozyme) based on a signal-on sensing mechanism. To realize the bridge between the gold substrate and graphene film, a monolayer of 4-aminothiophenol is self-assembled on the substrate, which is then served as connectors for the growth of 3D GFs on the gold substrate by the hydrothermal reduction (HR) technique. Moreover, given the excellent properties, such as enlarged surface area, strong binding strength between 3D GFs and gold substrate, and improved conductivity, the proposed 3D GF-fabricated gold substrate is readily employed to the construction of electrochemical biosensing platforms through introduction of magnetic nanoparticles (MNPs) as probe carriers. On the basis of the strand displacement reaction and specific binding between aptamer and its target, the developed biosensors achieve signal-on detection of microRNA-155 (miR-155) and lysozyme (Lyz) with high sensitivity and selectivity and further successfully applied to human serum assay. Overall, the proposed strategy for in situ growth of 3D GFs provides a powerful tool for a wide range of applications, which is not limited to electrochemical biosensors and can be extended to other areas, such as electrocatalysis and electronic energy-related systems.