The researchers explored the free convective flow of a hybrid nanofluid in a vertical microchannel with a rectangular cross‐section. Notably, both channel walls were heated alternately, and a transverse magnetic field was applied across the channel. The channel walls had unique properties, one of which was nonslip and the other was exceedingly hydrophobic. The major purpose was to investigate the effects of magnetism and superhydrophobicity on important flow parameters. The differential equations in the investigation were solved, producing accurate results. The study yielded some significant discoveries. First, when heated, the magnetic parameter reduced skin friction on both sides. Second, in both heating conditions, the magnetic field reduced flow rate and velocity. The flow rates in the two reported situations were similar at a crucial temperature jump coefficient. Furthermore, for low‐temperature jump coefficients, heating the superhydrophobic side reduced the Nusselt number whereas heating the nonslip side had no magnetic effect. The percentage change in the value of Nusselt number and velocity decreases continuously with increase in nonlinear density variation with temperature (NDT) parameter and magnetic parameter. The percentage increases in the value of skin friction with increase in temperature jump and slip length but decrease in the percentage of skin friction for the effect of magnetic term and NDT parameter. As the NDT parameter increases, the velocity percentage rises to 50.59% when the superhydrophobic surface is heated and to 84.30% when the nonslip surface is heated. The temperature jump is statistically significant for the value of the Nusselt number and skin friction for the no‐slip surface condition. These discoveries have practical consequences for the design and management of both tiny and large‐scale systems, with possible applications in microfluidics, microelectronics, nanoscience, and nanotechnology.