Five kinds of lightweight aggregate (LWA) cement mortars with different volume replacement ratios were prepared by the equal volume replacement method. The influence of LWA on the mechanical properties and capillary water absorption of cement mortar was tested using compressive, flexural strength test and weighing method. Based on the low-field nuclear magnetic resonance (LF-NMR) and scanning electron microscopy (SEM), the microstructure characteristics of LWA were analyzed. The results show that the weak mechanical strength of LWA affects the overall mechanical properties of cement mortar. As the replacement ratio of LWA increases, the compressive strength of the mortar decreases correspondingly. The capillary water absorption decreases with the increase of the replacement ratio and the age of LWA mortar. LF-NMR test data shows that the volume fraction of small pores decreases with the increase in the replacement ratio of LWA, and the volume fraction of medium and large pores is positively correlated with the replacement ratio. As the age increases, the amplitude of the signal amplitude representing the small pores decreases. The analysis of the interface transition zone (ITZ) of LWA mortar with SEM images indicates that the structure of the LWA mortar ITZ is relatively dense. At the same time, because the hydration product blockes the microporous surface of LWA, the impermeable boundary and internal closed pores are formed. The mortar mixed with LWA exhibits the characteristics of high porosity and low permeability during the capillary water absorption process.