The present invention relates to a 3-D waveguide coupling device capable of two-step coupling and a manufacture method thereof, the 3-D waveguide coupling device comprises: a first substrate, at least one waveguide layer, at least one assisting grating, at least one coupling material layer, and at least one 3-D tapered structure layer, wherein 3-D waveguide coupling device is able to couple the light into the waveguide layer by way of two-step coupling through the 3-D tapered structure layer, the coupling material layer and the assisting grating. Moreover, the light can also be coupled out from the waveguide layer through the assisting grating, the coupling layer, and the 3-D tapered structure. The manufacture method is adapted to fabricate the 3-D waveguide coupling device capable of two-step coupling via the present semiconductor process technology without increasing any other new equipment.