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Fused silica with surface structures has potential applications in microfluidic, aerospace and other fields. To fabricate structures with high dimensional accuracy and surface quality is of paramount importance. However, it is indeed a challenge to strike a balance between accuracy and efficiency at the same time. Here, a temporally shaped femtosecond laser Bessel-beam-assisted etching method with dual-control of incubation effect is proposed to achieve this balance. Instead of layer-by-layer ablation continuously with Gaussian pulses, silica is modified discretely by double pulse Bessel beam with one single layer. During the modification process, incubation effect is dual-controlled in single shot process and spatial scanning process to generate even modified region efficiently. Then, the modified region is etched to form designed structures such as microholes, grooves, etc. The proposed method exhibits high efficiency for fabrication of surface structures in fused silica.