In this research, the fluid flow and heat transfer phenomena within wavy multilayer microchannels comprising variable wavelength and amplitude are studied in laminar flow regime. In the present work, friction factor, Nusselt number and also overall performance of the multilayer microchannel are studied at different wavelengths and amplitudes and also Reynolds numbers. Numerical findings show that an increase in the number of layers results in the increase in the friction factor and Nusselt number. It is shown that the lowest and highest friction factors correspond to the cases of increasing amplitude and increasing wavelength, respectively. It is found that the decreasing wavelength and increasing amplitude cases result in the highest Nusselt number and increasing wavelength configuration leads to the lowest Nusselt number. Results exhibit that, with increasing the Reynolds number, the friction factor depending on the number of layers may increase or decrease whereas the Nusselt number increases. Numerical results show that for one-, two- and three-layer channels, the minimum relative friction factors are 0.1%, 3.7% and 4.7%, and maximum relative Nusselt numbers are 18.2%, 45% and 45.2%, respectively. It is also shown that an increase in the number of layers and Reynolds number causes the channel overall performance to increase. The lowest overall performances is associated to the increasing wavelength structure and the highest overall performance corresponds to the increasing amplitude configuration. It is shown that for one-, two- and three-layer wavy channels, the maximum overall performances are found to be 1.16, 1.43 and 1.43, respectively.