Thiourea is used in agriculture and industry as a metal scavenger, synthetic intermediate, and nitrification inhibitor. However, in wastewater, it can inhibit the nitrification process and induce the collapse of the nitrification system. In such a case, ammonia-oxidizing bacteria (AOB) lose their ability to remove ammonia. We investigated the nitrification system of a 60,000-t/d municipal sewage treatment plant in Nanjing, which collapsed after receiving 5–15 ppm (5–15 mg/L) thiourea. Ammonia nitrogen removal quickly recovered to more than 95% after inoculation with 10 t high-efficiency nitrification sludge, which was collected from a kitchen waste treatment plant. A heterotrophic nitrification strain was isolated from the inoculated sludge and identified as wild Pseudomonas by 16S rDNA sequencing and named “BT1.” Based on thiourea tolerance tests, BT1 can tolerate a thiourea content of more than 500 ppm. For comparison, the in situ process was imitated by the simulation system, and the wastewater shocked by 10 ppm thiourea could still meet the emission standard after adding 1% (V/V) BT1. High-throughput sequencing analysis was applied to study microbial succession during thiourea shock loading. The results showed that Hydrogenophaga and Thiobacillus grew with the growth of BT1. Pseudomonas BT1 was used for a 6,000-t/d printed circuit board (PCB) wastewater treatment system, the nitrification system returned to normal in 15 days, and the degradation rate stabilized at more than 95%.