In this paper, the microstructure and resistance to chloride ion penetration of ultra-high-performance concrete (UHPC) prepared from lightweight aggregate (LWA) were studied through simulation and experiment. The effects of LWA with different particle sizes on the chloride ion transport properties of lightweight ultra-high-performance concrete (L-UHPC) were discussed through simulation test results. The random delivery model of LWA in L-UHPC was established by MATLAB, and the model was introduced into COMSOL. Through the comparative analysis of experimental data and simulation results, the repeatability of the proposed model and the simulation accuracy were verified. The results show that when the LWA particle size changes from 0.15–4.75 mm to 0.15–1.18 mm, the width of interfacial transition zone (ITZ) and the overall porosity of L-UHPC decrease. This is because the large particle size LWA has more open pores with larger pore diameters and related interconnections, which are potential channels for chloride ion transport. Therefore, the chloride ion transport properties in L-UHPC are inhibited, which is manifested by the “tortuosity effect” of the LWA.