As a metal three-dimensional (3D) printing technology, selective laser melting (SLM) has been extensively applied to manufacture complex-shaped parts in industries. It is well known that the naturally formed surface by SLM processing is usually rough and irregular. The effects of the rough surface on heat transfer and fluid flow cannot be neglected when SLM is applied to fields such as heat exchangers and cooling equipment. In this paper, a novel bottom-up approach was proposed to build the naturally formed rough surface by SLM 3D printing. Numerical investigation on pressure loss and heat transfer characteristics of rectangular channels has been carried out based on the naturally formed rough model. Constant thermal boundary and symmetry boundary conditions were employed in the procedure of numerical computation. For comparison, a variety of typical surfaces with different roughness elements in previous studies have been introduced and analyzed. Results confirmed that the proposed rough surface modeling method was fully capable of descripting the real 3D-printed surface topography. Compared with the smooth surface, the heat transfer capacity of the 3D-printed rough channel was increased by 8.99%, while the pressure loss was increased by 25.02%. Additionally, 3D-printed rough surface had better overall thermal performance compared to rough surfaces with regular roughness element.