The magneto thermodynamic aspects of micropolar fluid (blood model) through an isotropic porous medium in a nonuniform channel with rhythmically contracting walls have been investigated. The flow analysis has been discussed under long wavelength and low Reynolds number approximations. The closed form solutions are obtained for velocity components, microrotation, heat transfer, as well as the wall vorticity. The modified Newton–Raphson method is used to predict the unsteady flow separation points along the peristaltic wall. Numerical computations have been carried out for the pressure rise per wavelength. The study shows that peristaltic transport, fluid velocity, microrotation velocity, and wall shear stress are significantly affected by the nonuniform geometry of the blood vessels. Moreover, the amplitude ratio, the coupling number, the micropolar parameter, and the magnetic parameter are important parameters that affect the flow behavior.