The middle layer water intake is one of main engineering measures for intercepting oncomelania snails, and it is a key structure for preventing snails dispersion through sluice gates. The middle layer water intake structure for oncomelania snails subsists some problems in practice. For example, snails with floating debrises will be absorbed into pipe by vertical-axis vortex. So the flume test was done to study the formation mechanism of the vertical-axis vortex and vortex elimination measures. The simple and effective measures to eliminate vortex have been suggested. The study results show that there exists the vortex in the upper water area with an angle 30 degree against vertical direction, and a cross beam set in the water area is an effective measure for eliminating vortex of the water intake.