Infection is one of the common complications in patients with nephrotic syndrome, and it is also an important cause of death. Early and accurate diagnosis of infectious pathogens is helpful for targeted treatment and improving the prognosis of patients. Nowadays, the main method of pathogen detection is culture method, the positive rate of pathogen detection is low because of immunosuppression of patients and the influence of different sampling and detection methods. High-throughput sequencing technique effectively complements the shortcomings of traditional culture methods with its advantages of rapidness, sensitivity and wide coverage. This paper reports one case of nephrotic syndrome complicated with cryptococcal infection and one case complicated with Stenotrophomonas maltophilia meningitis confirmed by high-throughput sequencing, suggesting that high-throughput sequencing technique has significant advantages and great application value in the diagnosis of nephrotic syndrome complicated with infection which is negative through traditional pathogen culture.