A major challenge in myocardial tissue engineering is replicating the heart’s highly complex three-dimensional (3D) anisotropic structure. Heart-on-a-chip (HOC) is an emerging technology for constructing myocardial tissue in vitro in recent years, but most existing HOC systems face difficulties in constructing 3D myocardial tissue aligned with multiple cell layers. Electrospun nanofibers are commonly used as scaffolds for cell growth in myocardial tissue engineering, which can structurally simulate the extracellular matrix to induce the aligned growth of myocardial cells. Here, we developed an HOC that integrates multi-layered aligned polycaprolactone (PCL) nanofiber scaffolds inside microfluidic chips, and constructed 3D thick and aligned tissue with a layered seeding approach. By culturing human-induced pluripotent stem-cell-derived cardiomyocytes (hiPSC-CMs) on chip, the myocardial tissue on the two layered nanofibers reached a thickness of ~53 μm compared with ~19 μm for single-layered nanofibers. The obtained myocardial tissue presented well-aligned structures, with densely distributed α-actinin. By the third day post seeding, the hiPSC-CMs contract highly synchronously, with a contraction frequency of 18 times/min. The HOC with multi-layered biomimetic scaffolds provided a dynamic in vitro culture environment for hiPSC-CMs. Together with the layered cell-seeding process, the designed HOC promoted the formation of thick, well-aligned myocardial tissue.