Mn4+ activated fluoride red phosphors, as candidate red materials in white light-emitting diodes (WLEDs), have received widespread attention. However, the poor water stability limits their application. Herein, a novel dodec-fluoride red phosphor Na3Li3In2F12:Mn4+ with good waterproof stability was successfully synthesized by solvothermal method. The crystal structure, optical property, micro-morphology, element composition, waterproof property and thermal behavior of Na3Li3In2F12:Mn4+ phosphor were analyzed. Under the 468 nm blue light excitation, the Na3Li3In2F12:Mn4+ phosphor has narrow emission bands in the area of 590–680 nm. Compared with commercial red phosphor K2SiF6:Mn4+, the Na3Li3In2F12:Mn4+ phosphor possesses better waterproof stability. When soaked in water for 360 min, the PL intensity of the Na3Li3In2F12:Mn4+ phosphor remains at initial 80%. Finally, warm WLEDs with CRI of 87 and CCT of 3386 K have been fabricated using blue InGaN chip, YAG:Ce3+ yellow phosphor and Na3Li3In2F12:Mn4+ red phosphor.