Nanoporous materials (sub-10 nm in diameter) have potential applications in chips, biosensors, thermoelectrics, desalination and other fields due to their large surface-to-volume ratio. Thermal annealing is a preferred technique to precisely control the ultra-fine nanopore size. Here, the 3D morphological evolution of a membrane with periodic nanopores by thermal annealing is studied. It is found that the evolution is determined by the combination of the membrane thickness, the initial nanopore radius and the periodic length of the porous pattern, rather than the previously suggested ratio between the membrane thickness and pore radius. High-temperature annealing experiments and molecular dynamics simulations are performed to confirm the rationality of the newly proposed model. Energy analysis demonstrates that surface energy minimization is the driving force of the morphological evolution. The local minimum of energy in the new model provides the possibility of thermal stability of nanoporous silicon as a thermoelectric material. This study provides guidance for the mass production of nanoporous membranes with high-temperature annealing.