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In recent years, researchers have made significant strides in understanding the ion transport characteristics of nanochannels, resulting in the development of various materials, modifications, and shapes of nano ion channel membranes. The aim is to create a nanochannel membrane with optimal ion transport properties and high stability by adjusting factors, such as channel size, surface charge, and wettability. However, during the nanochannel film fabrication process, controlling the geometric structures of nanochannels can be challenging. Therefore, exploring the stability of nanochannel performance under different geometric structures has become an essential aspect of nanochannel design. This article focuses on the study of cylindrical nanochannel structures, which are categorized based on the different methods for generating bipolar surface charges on the channel's inner surface, either through pH gradient effects or different material types. Through these two approaches, the study designed and analyzed the stability of ion transport characteristics in two nanochannel models under varying geometric structures. Our findings indicate that nanochannels with bipolar properties generated through pH gradients demonstrate more stable ion selection, whereas nanochannels with bipolar properties generated through different materials show stronger stability in ion rectification. This conclusion provides a theoretical foundation for future nanochannel designs.