Herein, we show the ability to control nonlinear optical nanocrystal orientation and nanostructure orientation at the same time in the Li₂O-Nb₂O₅-SiO₂ glass by high repetition rate (100-500 kHz) femtosecond laser direct writing. A self-organized nanostructure with nanoscale phase separation, nonlinear optical nanocrystals embedded in an amorphous network, can be oriented by laser polarization. With the increase of laser power, three modified regimes are revealed. At low laser power, a modified amorphous structure is obtained and has higher HF etching rate than that of the glass substrate. At moderate laser power, polar axes of nanocrystals tend to be perpendicular to laser polarization direction. The range of pulse energy narrows dramatically with the increase of repetition rate. At high laser power, microcrystals are obtained and crystallization is very sensitive to writing mode (the angle between writing direction and laser polarization direction). These findings shed light on the comprehension of ultra-fast laser-matter interaction and provide a new path toward fabricating three-dimensional optical devices.