Numerical analysis has been performed to analyse the effect of non-uniform heating on heat transfer charecteristics for steady laminar flow through wavy channel. Heat transfer charecteristics has been analysed with different heat flux amplitude and phase difference of sinusoidal heat flux. We observe an intricate interplay between the amplitude and phase difference of heat flux profile on the thermal transport characteritics. The local heat transfer enhancement is highly sensitive with change in amplitude of the sinusoidal heat flux.. For zero phase difference of heat flux profile, all local minima are higher in comparesion with local minima of the corresponding reciprocal phase difference, while the decrease in local maxima is not monotonic. Decrease in amplitude of heat flux increases the average Nusselt number, while for same heat flux amplitude zero phase difference yields higher average Nusselt number.