Microscale heat transfer is vital for the performance of smart thermal devices like heat sinks, thermosyphons, and microheat pipes. This study introduces a biothermal pumping flow model based on a multi-membrane pumping mechanism that leverages microscale heat transfer. The model describes rhythmic contraction and relaxation of membranes, combined with electro-osmosis in Jeffery fluid flow within a vertical microchannel of finite length. Two membranes on the microchannel walls, with varying amplitudes, diameters, and phase lags, generate pressure that moves fluid in both directions through contraction and expansion cycles. The model is based on the conservation of mass and momentum, using a low Reynolds number approximation to capture microscale transport phenomena at biomedical scales. Dimensionless conservation equations are analytically solved under no-slip boundary conditions, with results computed in MATLAB for clarity. Axial velocity results are simulated and verified using the optimal homotopy analysis method. The model explores the influence of key parameters (UHS, me, λ, Gr, β) on pressure gradient, velocity distribution, volumetric flow rates, skin friction, Nusselt number, and stream function. The findings demonstrate that pressure from membrane motion is significantly affected by thermal effects and buoyancy forces, and flow and pumping characteristics are largely determined by the fluid's rheological qualities and the geometrical features of the membrane. This study provides novel ideas for enhancing the functionality and design of smart thermal devices while also advancing microscale heat transfer technology.