Objective To compare endoscopic sinius surgery plus middle meatus fenestration with endoscopic sinius surgery plus middle and inferior meatus fenestration for fungus ball maxillary sinusitis. Methods Applying a prospective randomized controlled trial, 80 patients with fungal ball maxillary sinusitis from January, 2010 to March, 2011 were collected and then divided into two groups, including experiment (40 cases) and control groups (40 cases). The trial group received endoscopic sinius surgery plus middle and inferior meatus fenestration, which the control group received endoscopic sinius surgery plus middle meatus fenestration. Then a follow-up was conducted from the end of surgery to February 28th, 2013. All patients took subjective and objective assessment before and after the surgery, including VAS, SNOT-20, Lund-Mackay CT system scores and Lund-Kennedy endoscopic mucosal score. Results with the trial group was superior to the control group in VAS score, SNOT rating and Lund-Kennedy mucosa score 6 months, 1 year, and 2 years after surgery (Plt;0.01). Lund-Mackay CT score of the control group was significantly higher than the trial group after 1 year of surgery (Plt;0.01). According to the Haikou standard to assess the efficacy of surgery, we found that the total effectiveness rate of the trial group (100.0%; recovery: 36 cases; improved: 4 cases) was higher than that of the control group (87.5%; recovery: 28 cases; improved: 4 cases), with a significant difference (P=0.021). Conclusion Endoscopic sinius surgery plus middle and inferior meatus fenestration with a lower reoccurrence rate is superior to endoscopic sinius surgery plus middle meatus fenestration for fungus ball maxillary sinusitis in clinical efficacy.