Endophthalmitis can be a devastating complication after cataract surgery. Therefore, this study sought to better understand the occurrence rate of acute-onset postoperative endophthalmitis after cataract surgery in Chinese small and medium-scale departments of ophthalmology, as well as identify its risk factors and assess the treatment options. This investigation revealed 52 postoperative endophthalmitis cases in 46,185 operations at 30 hospitals from 2011 to 2013, at an occurrence rate of 0.11%. A small cataract surgery volume of less than 500 cases per year (OR 2.21; p = 0.006), the absence of 0.5% povidone iodine (PVP-I) irrigation (OR 1.73; p = 0.046), and intraoperative posterior capsular rupture (PCR) with vitreous loss (OR 4.40; p = 0.034) showed statistically significant associations with endophthalmitis in the multivariate analysis. The rate of culture positivity was 44.2%, with Staphylococcus epidermidis being the most common organism isolated in China. More than 40% of the endophthalmitis cases were treated with a nonstandard antibiotics regimen, and only 32.7% of these had a visual acuity of better than 20/40. We concluded that the occurrence rate of acute-onset endophthalmitis following cataract surgery in Chinese small and medium-scale departments of ophthalmology lags behind the level of developed countries, as well as Chinese top eye centers. Overall, the use of 0.5% PVP-I irrigation seemed to be an effective measure to reduce the risk of the development of postoperative endophthalmitis.