In this work, expansion and contraction square channels were presented for honeycomb regenerators to recover more waste heat from flue gas. A 3D numerical model of unsteady heat transfer was built with ANSYS Fluent for the new type of regenerators and user-defined functions (UDFs) were compiled to express the changes of fluid type, inlet velocity and temperature, etc. due to the switch between the flue gas and air blows. The current numerical model was validated by comparing its predicted results to experimental data in the literature. With the present model, the effects of expansion and contraction angle (θ), pitch (S) and regenerator length (L) on the performances of heat transfer and flow resistance were investigated for the novel regenerators. Temperature contours were presented to discuss the physical mechanism for the performance enhancement of regenerators with the expansion and contraction square channels. Numerical results confirmed that the expansion and contraction channels can improve the performance of honeycomb regenerators effectively, and regenerator effectiveness was improved by about 5 percentage under the premise of a limited increment of pressure loss. Besides, it was found that the longer the new regenerator, the better heat transfer performance it had. For the regenerators with a constant L, when the θ (or S) was fixed, the heat transfer performance can become better with the increment of S (or θ). However, the overall performance of the regenerator with a big θ can be undesirable because of its large flow resistance. The current numerical study on the heat transfer enhancement of honeycomb regenerators via the secondary development of CFD software presented a new way for the optimal design and performance improvement of regenerative heat exchangers.