The lumped model of flow instability in parallel-rectangular channels under heaving condition based on Galerkin nodal method is built, in which the model of flow instability under static condition and the additional pressure drop generated by heaving condition is included and the effect of heaving condition on flow instability is analyzed theoretically in the present work. The results show that the amplitude of heaving condition has little effect on the flow instability; when the frequency of heaving condition is much larger or smaller than the system inherent frequency, the frequency has little effect on the threshold power, while when two of them are more or less the same, the threshold power will decrease. And when the system suffers asymmetric condition, the effect of heaving condition will increase significantly.