Suppression of magnetoresistance (MR) is meaningful for sensor applications to immure magnetic fields. Herein, we report the observation of suppressed MR in PtSe2 microflakes by introducing the antidot arrays (AAs). We have compared the magnetotransport properties of PtSe2 microflakes before and after milling of AAs. The enhanced resistivity and notable MR suppression were observed while the AAs are milled in the PtSe2 microflakes. Their physical mechanism has been ascribed to the enhanced electron scattering rate due to the additional electron-antidot interactions. This work gave an example to suppress MR in materials by introducing AAs, which may be useful for sensor applications in magnetic fields.