The invention relates to the technical field of flexible circuit boards, and provides a multi-layer flexible circuit board manufacturing method and a multi-layer flexible circuit board. The multi-layer flexible circuit board manufacturing method comprises the steps of preparing a top layer unit, and reserving a transition copper layer in a top layer single-layer area of the top layer unit; preparing an intermediate layer unit and a bottom layer unit, and windowing the bottom layer unit and the intermediate layer unit, wherein the width of the windowed bottom layer unit and intermediate layer unit is matched with the width of a top layer multi-layer area of the top layer unit; performing board overlaying and laminating, that is, overlaying the intermediate layer unit in the top layer multi-layer area, overlaying the bottom layer unit on the surface of the intermediate layer unit and then forming an intermediate flexible circuit board through the lamination; and carrying out pattern transfer, that is, forming a circuit pattern on the surface of the top layer unit and/or the surface of the bottom layer unit, removing the transition copper layer and forming a multi-layer flexible circuit board. The top layer single-layer area is provided with the transition copper layer, so that the strength and hardness of the single-layer area are enhanced, a problem of folding of the top layer single-layer area in the subsequent processing process is effectively solved, and the yield is improved.