The study of the boundary layer is considered one of the most important theories in the field of heat and mass transfer because of its important explanation that shows us the behavior of different surfaces while they are under the influence of the flow accompanied by different thermal forces. The study of corrugated surfaces is one of the engineering applications, such as flow in heat exchangers or solar cells or cooling processes during surface heat treatments. This model is also used in medical applications such as flow in arteries or movement in the intestines. So, the work deals with investigating the boundary layer surrounding a three‐dimensional sinusoidal pipe; the boundary layer was assumed to be filled with a hybrid nanofluid consisting of water +Cu nanoparticles as the main fluid, supported by a small concentration of Al2O3 or Ag nanoparticles. The boundary layer is described by a set of nonlinear partial differential equations due to the continuity, momentum, and energy equations, which are transformed into a set of dependently coupled nonlinear ordinary differential equations. The obtained system of equations was solved using numerical techniques. The behavior of the boundary layer under the varying types and concentrations of nanoparticles and the influence of the magnetic field has been depicted by a set of graphs and tables. With reference to some results, it is found that using 5% of nanoparticles of aluminum oxide raises the rate of cooling by 8% and using 5% of silver nanoparticles increases it by 5%.