The present disclosure provides a three-dimensional packaging method and a three-dimensional package structure of a photonic-electronic chip. The method includes: fixing an electronic chip on a first area of a first surface of a photonic chip; fixing a dummy chip on a second area of the first surface of the photonic chip, wherein the photonic chip is provided with an optical coupling interface at the second area, and the dummy chip has a cavity with a single-sided opening, and the opening of the cavity faces and covers an optical coupling interface.