Constructing three-dimensional (3D) aligned nanofiber scaffolds is significant for the development of cardiac tissue engineering, which is promising in the field of drug discovery and disease mechanism study. However, the current nanofiber scaffold preparation strategy, which mainly includes manual assembly and hybrid 3D printing, faces the challenge of integrated fabrication of morphology-controllable nanofibers due to its cross-scale structural feature. In this research, a trench-guided electrospinning (ES) strategy was proposed to directly fabricate 3D aligned nanofiber scaffolds with alternative ES and a direct ink writing (DIW) process. The electric field effect of DIW poly(dimethylsiloxane) (PDMS) side walls on guiding whipping ES nanofibers was investigated to construct trench design rules. It was found that the width/height ratio of trenches greatly affected the nanofiber alignment, and the trench width/height ratio of 1.5 provided the nanofiber alignment degree over 60%. As a proof of principle, 3D nanofiber scaffolds with controllable porosity (60-80%) and alignment (30-60%) were fabricated. The effect of the scaffolds was verified by culturing human-induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs), which resulted in the uniform 3D distribution of aligned hiPSC-CMs with ∼1000 μm thickness. Therefore, this printing strategy shows great potential for the efficient engineered tissue construction.