The paper theoretically investigates the heat transfer of nanofluids with different nanoparticles inside a parallel-plate channel. Second-order slip condition is adopted due to the microscopic roughness in the microchannels. After proper transformation, nonlinear partial differential systems are converted to ordinary differential equations with unknown constants, and then solved by homotopy analysis method. The residual plot is drawn to verify the convergence of the solution. The semi-analytical expressions between NuB and NBT are acquired. The results show that both first-order slip parameter and second-order slip parameter have positive effects on NuB of the MHD flow. The effect of second-order velocity slip on NuB is obvious, and NuB in the alumina–water nanofluid is higher than that in the titania–water nanofluid. The positive correlation between slip parameters and Ndp is significant for the titania–water nanofluid.