The effect of vertical throughflow and internal heating effects on fluid saturated porous medium under gravity modulation is investigated. The amplitude of modulation is considered to be very small and the disturbances are expanded in terms of power series of amplitude of convection. A weakly nonlinear stability analysis is proposed to study stationary convection. The Nusselt number is obtained numerically to present the results of heat transfer while using Ginzburg–Landau equation. The vertical throughflow has dual effect either to destabilize or to stabilize the system for downward or upward directions. The effect of internal heat source (Ri>0) enhances or sink (Ri<0) diminishes heat transfer in the system. The amplitude and frequency of modulation have the effects of increasing or diminishing heat transport. For linear model Venezian approach suggested that throughflow and internal heating have both destabilizing and stabilizing effects for suitable ranges of Ω. Further, the study establishes that heat transport can be controlled effectively by a mechanism that is external to the system throughflow and gravity modulation.