The invention relates to a manufacturing method of a three-dimensional heterogeneous integrated system. The method includes the following steps that: a silicon carbide-based substrate layer and a silicon carbide-based epitaxial layer are prepared; back through holes are separately formed in the silicon carbide-based substrate layer and the silicon carbide-based epitaxial layer, and at least one passive device is grown on the silicon carbide-based epitaxial layer, and active devices are prepared; at least one active device is bonded onto the silicon carbide-based substrate layer through using abenzocyclobutene polymer; and the silicon carbide-based substrate layer is in bonding connection with the silicon carbide-based epitaxial layer; and all the active devices are in bonding connection with the at least one passive device. With the manufacturing method provided by the embodiments of the invention adopted, the reliability of the technique processes of the devices is ensured, and the efficiency of the manufacturing of the devices is improved.