Ceratostigma willmottianum Stapf is a unique chalk gland (salt-excreting) plant from China, with a salt gland structure that excretes white crystals of calcium carbonate (CaCO3), which has potential biomineralization and carbon sequestration functions. Due to the narrow distribution of wild germplasm resources, there is a lack of diversity of new varieties to satisfy commercial development and scientific exploration. Therefore, we used ethyl methanesulfonate (EMS) mutagenesis to obtain new dwarf mutant germplasm, and analysed it in terms of morphology, growth, photosynthesis, salt glands, and excretion traits. All four dwarfing mutant strains (DM1, DM2, DM3, and DM4) exhibited extreme dwarfing (62.28%, 62.28%, 74.55% and 61.68% reduction in plant height, respectively), faster growth, increased belowground root biomass, and earlier bud differentiation and flowering. Photosynthetic capacity was enhanced: chlorophyll content, maximum quantum yield of PSII (Fv/Fm), effective quantum yield of PSII (ΦPSII), photochemical quenching coefficient (qP), electron transfer rate (ETR), net photosynthesis (Pn), intercellular CO2 concentration (Ci), stomatal conductance (Gs), and transpiration (Tr), were significantly higher in leaves of DM mutants. The density of salt glands per unit leaf area and average Ca2+ excretion rate of individual salt glands increased significantly (especially in DM2), and CaCO3 accumulation per unit leaf area was 28.57% higher than that of the wild type. Pearson correlation analysis showed that photosynthetic capacity was significantly and positively correlated with CaCO3 excretion. The above study not only provided enriched new germplasm of C. willmottianum, but also important research material for studying the mechanism of CaCO3 excretion by salt glands and carbon sequestration capacity of biomineralization.