The invention discloses a novel sphingopyxis strain. The novel sphingopyxis strain is preserved in China General Microbiological Culture Collection Center (CGMCC) and is named as sphingopyxis YF1 (Sphingopyxis sp.YF1); and the preservation number is CGMCC No: 16341 and the preservation time is August 27, 2018. The strain has a very strong degradation effect on microcystin, can be applied to management of microcystin pollution and also provides a novel strain for the field of microcystin degradation. The invention further discloses application of the sphingopyxis strain to the microcystin degradation and detoxification field; the sphingopyxis YF1 is used for carrying out degradation and detoxification on the microcystin, the degradation speed is high and the microcystin can be completely degraded; the toxicity of the microcystin and degradation products thereof also can be eliminated; the problem that the toxicity of the microcystin cannot be completely eliminated by a current strain issolved; and the novel sphingopyxis strain has relatively high practical value and popularization and application value.