Scaffold plays an important role in tissue engineering (TE), which replaces the extracellular matrix (ECM), and mimics the environment where the tissue cells live in. various methods are employed to fabricate TE scaffold with controlled porosity. However, most of the existing scaffolds are in homogeneous structure, which are different from the actual target tissue. Herein, we developed melt electrohydrodynamic (EHD) printing technique to fabricate TE scaffold with heterogeneous structure in layer-by-layer manner. Parameters (heating temperature, air pressure, collecting speed) were studied to stably print deposited PCL filaments in micro scale with controlled fiber diameters. In this paper, heterogeneous scaffolds were fabricated in two strategies, by changing fiber diameters and pore sizes. Scaffolds consist of the same pore size but different fiber diameters have heterogeneous mechanical properties. Different distribution of pore sizes can control cell growth in corresponding regions. Moreover, the cell proliferation and morphology experiment was conducted to prove the validity of the fabricated heterogeneous structure. It’s envisioned that the 3D printed heterogeneous scaffolds with high resolution can mimic the native tissue in both mechanical properties and architecture, thus provide a more in vivo like environment for tissue engineering.