The treatment of sphere contact is a crucial issue on the numerical analysis of the flow and heat transfer in packed beds of particles. In this work, the effects of three different methods including introducing a gap, area contacting and cylindrically bridging on the flow and heat transfer performances of structured packed beds of particles are investigated with CFD methods. The simulation results have shown that the influence of different treatment methods on the contact point on flow and heat transfer gets greater as the porosity decreases and the Reynolds number increases. There are no large differences among these three methods on the pressure drop and heat transfer under laminar flow regime. Compared with the experimental results, cylindrically bridging method is proved to be reasonable to simplify the sphere–sphere contact points. Therefore, cylindrically bridging treatment method is encouraged to be used instead of point contact method between particles with CFD analysis in structured packed beds of particles.