The local superhydrophobic micro channels were fabricated by BNNTs growth with the method of ball milling assisted with B ink annealing. Both the ball milling and annealing processes in the preparation were optimized to obtain high quality and density of BNNT films. The structure of anode plate is designed to synthesize BNNTs selectively under control. Besides, the customizable growth by the calculation of flow model in COMSOL as well as surface treatment were achieved to further reduce the hydro-resistance. This study exhibits the predictability and controllability of BNNTs growth in customizable microstructures.