With the ever-increasing energy costs, the need to improve the efficiency of cooling systems, reduce costs, and optimize the design is usually the first goal for system designers. One way to improve these systems is to use nano-refrigerants (NRs). This study simulates the thermal manner of ammonia refrigerant with Cu nanoparticles (NPs) in a nanochannel (NC) by calculating parameters such as velocity (V) and temperature (T) profiles, aggregation time (AT), and heat flux (HF). The result shows that by increasing the electric field amplitude (EFA) from 1 to 5 V/m, the maximum V and maximum T increase from 0.00086 Å/ps and 240 K to 0.00089 Å/ps and 245 K, respectively. With increasing the external EFA to 5 V/m, the HF value converges to 1395 W/m2, and the AT decreases to 3.90 ns. On the other hand, the change in maximum V in the samples with the pyramid, half-spherical (HS), and rectangular cubic (RC) cavities reached 0.74000 Å/ps, 0.00072 Å/ps, and 0.6565 Å/ps, respectively, and the maximum T changes to 232 K, 238 K, and 235 K in the RC, HS, and pyramid cavities samples. The results show that the structure has a higher HF in the presence of the RC cavity. So, the HF and AT values for samples with RC cavities are 1650 W/m2 and 4.59 ns, respectively.