The invention discloses a manufacturing method of a three-dimensional stacked radio frequency optical module. The manufacturing method specifically comprises the following steps that: 101) a radio frequency adapter plate manufacturing step; 102) a heat dissipation adapter plate manufacturing step; 103) a multi-layer bonding step; 104) a sealing cover adapter plate manufacturing step; 105) a chip communication step; and 106) a module bonding step. According to the method of the invention, chips with large areas are placed in a vertical direction through a multi-layer stacking process; the electric signals of the chips are led out through a TSV process; photoelectric chips are arranged at the tops of modules, so that radio frequency signals are transmitted out or connected into the modules in the form of optical signals; and therefore, the integration degree of the optical module can be greatly increased.