Alga contamination was a major problem in microalgae open cultivation. The objective of this study was to estimate the effect of silicon on microalgae growth by mixed-culture experiments with four different microalgae. The results showed that under the osmotic pressure caused by high concentration of Na2SiO3, Navicula sp. N6 had a competition advantage of absorbing nutrient compared with the other three microalgae. The impacts (initial pH, nitrogen content, and silicon content) on cell growth and lipid accumulation were investigated by response surface analysis and the biomass and lipid content increased from 1.01 g/L and 10.98% to 1.33g/L and 20.04% under the optimal conditions, with lipid yield raised by 142%. Comparison on the growth under optimum and silicon deficiency condition indicated that silicon played an important role on the growth of Navicula sp.N6 and algal contamination in diatom open scale cultivation could be solved by regulating the sodium silicate concentration.