[Background] Due to excellent growth performances, clear genetic backgrounds and mature genetic manipulations, Escherichia coli typical strains are commonly selected for producing β-farnesene, but the yields of β-farnesene still cannot meet the needs of industrial production until now. [Objective] Combined mutagenesis breeding techniques were used to obtain β-farnesene producing strains with high yields. [Methods] Escherichia coli EC-16 was bred by combination mutation methods of atmospheric and room temperature plasma (ARTP) and ultraviolet (UV), through the first screening with isopentenyl pyrophosphate (IPP) screening plate as selection pressure and the following second screening step with flask fermentation culture, finally subjected to fermentation tank verification. The genetic stability of the highly productive mutant strains was carefully comparatively tested by continuous multi-generation cultured. [Results] A mutant strain named E. coli HVK-9 was obtained and the yield of β-farnesene reached up to 22.1 g/L, which was 168.74% higher than that of the original strain. [Conclusion] The combinational mutations by virtue of ARTP-UV with isopentenyl pyrophosphate resistance screening model in this study can significantly improve the positive mutation rates, which can finally confirm the effectively increase with the yield of β-farnesene. The mutant strain HVK-9 has good genetic stability as an industrial fermentation strain, which lays a good foundation for the industrial production and application of β-farnesene.