The invention provides a Thermoactinomyces-vulgaris-containing desilting agent which comprises a biocatalyst, a nonionic surfactant, an aloe extracting solution, a purslane extracting solution, a Herba Centellae extracting solution, a bioenzyme activator, borax, shikimic acid, humic acid, a vitamin complex, a substrate, a porous sodium-type activated zeolite powder carrier, halophile, Thermoactinomyces vulgaris and a crosslinking agent. The invention also provides application of the Thermoactinomyces-vulgaris-containing desilting agent in salt drainage concealed pipes. The desilting agent lowers the salt content of water in the salt drainage concealed pipe, and the salt content of water at the outlet of the salt drainage concealed pipe is lowered to 0.49-0.61%. The desilting agent lowers the plugged hole percentage of the salt drainage concealed pipe, and the plugged hole percentage of water in the salt drainage concealed pipe is lowered to 11-12%. The desilting agent enhances the saline-alkali soil silt treatment speed, and the time for treating 8cm-thick saline-alkali soil silt is 6-7.0 days. The desilting agent has favorable desilting effect; and one year after desilting, the water transparency is up to 10-12cm, whereas the transparency of the control group is 5cm.