Strobilurins are one of the most important classes of agricultural fungicides. To discover new strobilurin analogues with high activity against resistant pathogens, a series of new strobilurin derivatives bearing structurally diverse heterocycle side chains 3a-m and 4a-g were designed and synthesized via a microwave-assisted procedure. The advantages, such as good to excellent yields, shorter reaction times, mild reaction conditions, and simple purification procedures, distinguish the present synthetic protocol as a highly efficient method for the preparation of strobilurin thioether derivatives. Bioassays indicated that most of the compounds showed broad-spectrum fungicidal activity in vitro. Interestingly, as compared to the control of a commercial strobilurin fungicide, Kresoxim-methyl, compounds 3b, 3g, 4c, and 4d possessed remarkably higher in vitro fungicidal activity against six kinds of tested fungi. Exhilaratingly, compound 3g exhibited higher in vivo activity against Sphaerotheca fuliginea and Pseudoperoniospora cubensis than Kresoxim-methyl, and the in vivo fungicidal activities of compound 4d and Kresoxim-methyl against S. fuliginea and P. cubensis are at the same level. The present work demonstrated that strobilurin analogues containing benzothiazole side chains could be used as a lead structure for further developing novel fungicides.