A novel three-phase hollow fiber liquid phase microextraction was developed for the determination of malachite green (MG) in environmental waters, which selected [BMIM][$PF_6$] mixed with 1% trioctylphosphine oxide (TOPO) as supported phase. Several parameters (accepter phase pH, sample pH, supported phase membrane, volume of accepter phase, salinity, extraction time) that could affect extraction performance were investigated. Under the optimal extraction conditions, the established approach showed excellent characters as: high enrichment factor (212), wide linear range ($0.20-100{mu}gL^{-1}$), low detection limit ($0.01{mu}gL^{-1}$), good reproducibility (RSD, 8.9%, n=5) and satisfactory recovery (84.0-106.2%). The method was applied to detect MG at Yangtze River and pond waters in Zhenjiang, Jiangsu province, and 4 sites among 15 sampling sites were found MG with the concentration of $1.73-11.06{mu}gL^{-1}$, which confirmed that the proposed environmentally friendly method was simple and effective for monitoring MG in aquatic system.