A fused silica glass micro-channel can be formed by chemical etching after femtosecond laser irradiation, and the successful etching probability is only 48%. In order to improve the micro-channel fabrication success probability, the method of processing a high-temperature lattice by a femtosecond laser pulse train is provided. With the same pulse energy and scanning speed, the success probability can be increased to 98% by optimizing pulse delay. The enhancement is mainly caused by the nanostructure, which changes from a periodic slabs structure to some intensive and loose pore structures. In this Letter, the optimum pulse energy distribution ratio to the etching is also investigated.