In order to prepare a lightweight gypsum mortar with stable performance, low density and high strength, further expand the use of FGD building gypsum and improve the utilization rate of FGD building gypsum. In this paper, based on the cementitious material (GM-PO-S95 system) prepared from desulfurized building gypsum (FGD gypsum) as the main raw material, the experimental design was carried out with two kinds of lightweight aggregates ( Eubert Perlite (EP), Vitrified Microbeads (VM)). The low-density and high-performance gypsum-based lightweight mortar was prepared by analyzing the mechanical properties, density, water resistance, and microscopic morphology and pore size distribution of the lightweight gypsum mortar. The study showed that: the density of the specimen decreased significantly after adding lightweight aggregate, and the 3d density decreased to 715kg/ m^3 at 20% VM admixture, which was decreased by more than 60%; while the density decreased, the mechanical properties were still good, with the compressive strength maintained at 12MPa, flexural strength maintained at 2.8MPa, and the water absorption rate decreased to about 26%; the addition of VM, together with the hydrated gypsum crystals of GM-PO-S95 system, not only reduces the ratio of pore size distribution, but also gypsum crystals enter into the interior of glass beads, interact with glass beads, and together hold up the internal structure of lightweight gypsum mortar.