Invasive fungal disease (IFD) has high morbidity and mortality, the spectrum of pathogenic fungi and high-risk groups have also changed. Fewer literature focus on the overall incidence of IFD in various departments of general hospitals. Among the adult inpatients in four Chinese tertiary hospitals located in Beijing, Shanghai, Nanning and Nanchang, proven or probable cases of IFD were included prospectively in this study between May 1, 2021 and May 1, 2022. The clinical data were collected and analyzed. A total of 330 patients (342 episodes) with 278 of proven and 64 of probable IFDs were included, including invasive candidiasis (IC) (132, 40.0%), cryptococcosis (64, 19.4%), invasive aspergillosis (IA) (54, 16.4%), Talaromyces marneffei (TsM) infection (43, 13.0%), Pneumocystis pneumonia (PCP) (16, 4.8%), mixed fungal infection (10, 3.0%), other mold or yeast infection. 37.9% occurred in elderly patients (age ≥ 65 years). Nosocomial infection accounted for 44.5%, the proportion of nosocomial infection was highest in patients with IC (81.8%). Diabetes (19.7%) was the most common underlying disease. 83.9% of the 342 episodes of IFD had evidence of fungal culture, while the proportion of microscopic examination and histopathology as mycological evidence was 26.9% and 3.5%, respectively. The cumulative all-cause mortality at 180 days after diagnosis of IFD was 38.5%. Age ≥ 65 years old (HR = 1.670, P = 0.009), ICU (HR = 2.002, P = 0.001), nosocomial infection (HR = 1.630, P = 0.016) and diabetes (HR = 1.679, P = 0.013) were associated with increased death in IFD patients. The prognosis of IFD patients was poor. Doctors should pay attention to nosocomial fungal infection especially in old and diabetes.