Truss-type lattices present good mechanical and thermal properties and are regarded as promising structures for internal cooling. This study presents a systematic comparison of thermo-fluid behaviors among staggered pin fin array, Kagome lattice array and Body Centered Cubic (BCC) lattice array in a rectangular channel under an identical porosity. Transient liquid crystals (TLC) and numerical methods were utilized to explore the flow and endwall heat transfer characteristics in structures. The results reveal that, due to stronger flow mixing and more irregular vortices, the endwall-averaged Nusselt number of the Kagome array and the BCC array is 17–24% and 26–41% higher than that of the pin fin array, respectively. The similar topology results in similar heat transfer characteristics between the Kagome array and the BCC array, and an arc-shaped high heat transfer wake region outside the vertex is induced by the horseshoe vortex and the secondary flow washing the endwall. Meanwhile, for the Kagome array, a strong counter rotating vortex is formed near the bottom endwall, while in contrast, there is no obvious similar flow behavior near the top endwall. This leads to a 46–54% difference in the Nusselt number between the bottom endwall and the top endwall of the Kagome. In addition, the relationship between the element-averaged Nusselt number and Reynolds number of each array is obtained to guide practical applications. This research indicates that BCC or Kagome lattices may become a potential alternative to conventional pin fins due to their higher thermal efficiency.