The current study investigates how blue energy generation within a charged nanochannel is influenced by nanochannel deformation upon a salinity gradient. We developed the mathematical framework for fluid-structure interaction using a finite-element method-based solver. The results show that the higher pressure produced by the greater salt concentration under the lower modulus of elasticity causes a significant deformation of the nanochannel wall near the entrance. For the lower modulus of elasticity, the degree of electrical-double layer (EDL) overlap decreases accordingly. This, as a result of the reduced ionic current, leads to a decrease in the ionic selectivity of the nanochannel. It is seen that for a lower mechanical strength of the channel wall material, the maximum power density and energy conversion efficiency under the salinity gradient become lower. Based on the findings, in order to achieve the highest power density and efficiency, the strength of the nanofluidic device needs to be improved.