The structural evolution of flexible nanochannels within a 2D material membrane, influenced by the ingress of water molecules, plays a crucial role in the membrane's filtration and structural stability. However, the experimental observation of nanoscale water is challenging, and current studies mostly focus on rigid nanochannels. Further investigation on the nanoconfined water is urgently needed, considering the flexibility and deformation of the channel. In this work, MD simulations and theoretical analyses are conducted to investigate the water structure and thermodynamic properties when confined within both rigid and flexible graphene/graphene oxide (GO) nanochannels. In free rigid graphene nanochannels, the interlayer distance exhibits a quantized increase with the number of water molecules, along with sudden changes in entropy, potential energy, and free energy of the water molecules. Meanwhile, in flexible graphene nanochannels, the average interlayer space increases linearly with the number of water molecules. In free rigid GO nanochannels, with the increase of oxidation concentration, the quantized increase in the interlayer space gradually diminishes, accompanied by a decrease in both potential energy and free energy. This work provides insights into the configurational evolution of flexible nanochannels within water, offering guidance in fields such as desalination and mass transport of 2D material membranes.