In order to realize a high-integration and high-stability three-dimensional optical chip, it is necessary to systematically study the coupling characteristics of three-dimensional spatial waveguides. This paper mainly studies the coupling between waveguides in three-dimensional integrated optical chips. The electromagnetic field distribution of the waveguide array under different architectures is simulated by full-wave simulation. The coupling efficiency between parallel waveguides and crossed waveguides is analyzed, which is related to and the waveguide spacing, the refractive index of the surrounding medium, the working wavelength and the angle. In parallel waveguides, when the center-to-center spacing between the waveguides on two SiO₂ substrates is 0.76 μm and the coupling length is 72.5 μm, the coupling efficiency between the waveguides in the vertical direction reaches 0.997. In crossed waveguides, the coupling efficiency between the waveguides is very sensitive to the angle between the waveguides. When the angle is greater than 10°, no coupling occurs between the waveguides, so the coupling between the waveguides can be controlled by adjusting the angle between the waveguides.