In order to improve the possibility of successful bonding and performance of structures, the new method for multi-depth silicon etching is required. This paper aims to design and create a new method for one-time multi-depth silicon etching in manufacturing complex structures based on SiO2 masking layer. The core idea of this method is that: Firstly, all patterns are transferred into photo resist through photo etching; Then etch pattern will be transferred in the SiO2 masking layer by multi-time shallow etching with different time etching control; Finally, patterns will be transferred to the silicon wafer with uniform ratio based on the measured etching selectivity of SiO2-Si with one time. In the experiments, the process is completed in the silicon wafer with SiO2 masking layer whose thickness is elaborately designed. Firstly, the etching rate of SiO2 and the etching selectivity of SiO2-Si were measured accurately. Secondly, the shallow structure based on the designed structure, the etching rate of SiO2 and the etching selectivity of SiO2-Si is etched on the SiO2 masking layer. The second step forms different thickness version of SiO2 masking layer. At last, the SiO2 masking layer is etched until final structure and consequently different depth of groove accomplish due to various thickness of SiO2 etched by previous step. The experimental results indicated that the new methods has at least three advantages compared to traditional method: That is faster efficiency, higher cleanness and more complex structure. Fast work efficiency owes to only SF6 etching rather than two gases of SF6 and C4F8 to reduce half of time. Also high cleanness comes from being not exposed to air and researchers directly. The largest benefit of new method may be that can create more complex structure for higher required machine design and for higher mechanical function. It is because that normal etching method could only build few different depth of grooves due to multi-process limitation and contrary to normal one, new method can create more different depth of groove. And more different depth of groove means that more complex structure can be designed.