Customized heat treatment is essential for enhancing the mechanical properties of additively manufactured metallic materials, especially for alloys with complex phase constituents and heterogenous microstructure. However, the interrelated evolutions of different microstructure features make it difficult to establish optimal heat treatment processes. Herein, we proposed a method for customized heat treatment process exploration and establishment to overcome this challenge for such kind of alloys, and a wire arc additively manufactured (WAAM) Mg-Gd-Y-Zn-Zr alloy with layered heterostructure was used for feasibility verification. Through this method, the optimal microstructures (fine grain, controllable amount of long period stacking ordered (LPSO) structure and nano-scale β′ precipitates) and the corresponding customized heat treatment processes (520 °C/30 min + 200 °C/48 h) were obtained to achieve a good combination of a high strength of 364 MPa and a considerable elongation of 6.2%, which surpassed those of other state-of-the-art WAAM-processed Mg alloys. Furthermore, we evidenced that the favorable effect of the undeformed LPSO structures on the mechanical properties was emphasized only when the nano-scale β′ precipitates were present. It is believed that the findings promote the application of magnesium alloy workpieces and help to establish customized heat treatment processes for additively manufactured materials.