Enhancing the heat transfer rate using nanofluids is of great interest to engineers and scientists. This research aims to study the heat and mass transfer analysis of three-dimensional squeezing carbon nanotube- (CNT-) based nanofluid flow inside a rotating stretching channel. The upper wall of the channel is assumed to have a reciprocating movement, and the lower wall is assumed to be stationary and permeable. Also, radiative effects are taken into account using the Taylor series approximation. The momentum and energy equations are transformed into a coupled system of nonlinear ordinary differential equations utilizing similarity solutions. A new multiscale and accurate method was developed to solve the achieved nonlinear systems of equations. Water is chosen as the base fluid; single-wall carbon nanotubes (SWCNTs) and multiwall carbon nanotubes (MWCNTs) are added to it, and then two types of nanofluids were created. The effect of different variables such as the concentration of nanotubes, nanotube’s type, suction parameter, rotation parameter, squeezing number, Eckert number, and radiation parameter on the velocity and temperature profiles is investigated. Our results reveal that the temperature profile is an increasing function of the squeezing number, suction, rotation, and radiation parameters when the upper wall moves towards the lower one.