Gas transport through nanochannels, a type of free molecular flow, is ubiquitous in nature and possesses considerable significance in industrial fields, including membrane separation and vacuum technology. The Knudsen theory, which serves as the fundamental framework of free molecular flow, assumes that gas molecules undergo diffuse reflections on the wall, and predicts the gas flux through nanochannels. However, numerous experiments have shown that gases can experience specular reflection on some material surfaces, resulting in notably higher gas flux than the prediction of Knudsen theory. In our study, we investigated the impact of wall morphology and gas molecular geometry on the gas-wall interaction, demonstrating the crucial role of atomic configuration. Furthermore, we proposed an improved Knudsen theory capable of characterizing the gas flux of free molecular flow, compatible with any degree of surface roughness. Our work deepens the understanding of gas-wall interactions at the atomic scale and provides a theoretical basis of free molecular flow incorporating both specular and diffuse reflections. These findings may improve predictions and optimizations in fields such as microfluidics, vacuum technology, and gas separation processes.