Disclosed is a microwave chemical method for totally extracting fluorine and rare earth from bastnaesite concentrate, including: alkaline conversion defluorination of bastnaesite through microwave irradiation, microwave-assisted leaching of fluorine, solid-liquid separation of leaching solution and microwave-assisted leaching of rare earth. The rare earth hydrochloric acid solution for leaching contains no fluorine ion, so that the fluorine interference of subsequent processes such as impurity removal can be completely avoided; the fluorine and the rare earth are leached with microwaves, which does not need the stirring, so that the automatic control is easy to implement; the fluorine and rare earth leaching speed is high, the leaching time is short and the complete leaching of fluorine and little residual alkali in the slag can be realized by two-time leaching; and no fluorine-containing waste water is discharged, and the total extraction of the rare earth can be realized by one-time leaching.