With a prospective, randomized and double-masked control method, homoharringtonine(H.H) and 5-Fluorouracil (5-FU) were used in filtering surgery. We compared the effect and side effect of H.H with those of 5-FU. 24 eyes were in H.H group and 23 eyes in 5-FU group. An average follow-up of 18 months revealed: (1) the cumulative percentage of functioning bleb in H.H group (84.9%) was significantly higher than that in 5-FU group (62.2%) (P < 0.05); (2) the cumulative surgical success rate in H.H group (85.7%) was significantly higher than that in 5-FU group (61.1%) (P < 0.05); (3) the rate of corneal erosion in H.H group (20.8%) was significantly lower than that in 5-FU group (52.2%) (P < 0.05), the difference of other complications between H.H group and 5-FU group was not significant.