Low-temperature nitrogen adsorption is a widely used method for the research and evaluation of gas shale’s pore structure. The existing interpretation method, utilizing gas adsorption isotherms to obtain pore size distribution (PSD), is always based on the one-dimensional geometry model, while the void space of gas shale has strong multi-dimensional characteristics. It is necessary to investigate the nitrogen condensation and evaporation behavior in multidimensional structures. In this study, a series of two-dimensional and three-dimensional models based on ink-bottle pores were constructed. A hybrid molecular simulation approach combining grand canonical Monte Carlo (GCMC) and molecular dynamics (MD) is proposed to simulate the low-temperature nitrogen adsorption isotherms. Three aspects have been analyzed in detail. Compared with the conventional understanding that the threshold of cavitation in the ink-bottle pore only relates to throat diameter, this study discloses a wider and more comprehensive range of conditions of cavitation that considers both the throat length and diameter. As pore spaces of shale samples consist of many complex interconnected pores, the multi-stage ink-bottle pore model is more suitable than the single ink-bottle pore model to similarly reproduce the wider cavitation pressure range. A more universal parameter is proposed that quantitatively unifies the influence of cavity diameter and length on condensation pressure and has good applicability in cavities with different shapes. This work quantitatively studies the nitrogen adsorption isotherms of three-dimensional complex nanopore structures using molecular simulation and provides a reasonable explanation for the low-temperature nitrogen adsorption isotherms of gas shale.