To meet the demand for higher performance and wearability, integrated circuits are developing towards having multilayered structures and greater flexibility. However, traditional circuit fabrication methods using etching and lamination processes are not compatible with flexible substrates. As a non-contact printing method in additive manufacturing, electrohydrodynamic printing possesses advantages such as environmental friendliness, sub-micron manufacturing, and the capability for flexible substrates. However, the interconnection and insulation of different conductive layers become significant challenges. This study took composite silver ink as a conductive material to fabricate a circuit via electrohydrodynamic printing, applied polyimide spraying to achieve interlayer insulation, and drilled micro through-holes to achieve interlayer interconnection. A 200 × 200 mm2 ten-layer flexible circuit was thus prepared. Furthermore, we combined a finite element simulation with reliability experiments, and the prepared ten-layer circuit was found to have excellent bending resistance and thermal cycling stability. This study provides a new method for the manufacturing of low-cost, large-sized, multilayer flexible circuits, which can improve circuit performance and boost the development of printed electronics.