The quantum Toffoli gate is one of the most important three-qubit gates, but it is challenging to construct a chip according to the complicated traditional circuit. Using the optimized 3D configuration with an overpass waveguide to reduce the circuit complexity, we successfully fabricate an on-chip path encoded photonic quantum Toffoli gate enabled by the 3D capability of the femtosecond laser direct writing (FLDW) for the first time to our knowledge, whose truth-table fidelity is higher than 85.5%. Furthermore, a path encoded four-qubit controlled-controlled-controlled NOT gate is written to confirm the scalability of this resource-saving technique. This work paves the way for the FLDW of more complex and powerful photonic quantum computation chips.