This paper presents the synthesis of a waterproof geopolymer based on the modification of silicon phosphate (Si3(PO4)4) that adheres to alumina and quartz glass substrate, which can replace traditional organic polymers for packaging deep-ultraviolet light-emitting diodes. The waterproof property of geopolymer strongly depends on the Si3(PO4)4 loading amount due to its hydrolysate H+ substitutes Na+, which is vulnerable to water. FESEM and microhardness results show that aging by 85°C/85% relative humidity for 100 h, the optimal waterproof geopolymer adhesive is successfully synthesized when the mass ratio of metakaolin, water glass, and Si3(PO4)4 is equal to 0.48: 1: 0.08 respectively, and the corresponding adhesion strength of 6.41 MPa to alumina substrate is achieved after the reliability testing. The rheological properties show that the optimal waterproof geopolymer adhesive, with shear thinning behavior and good thixotropy, is suitable for processing while holding the original shape.