The magnetoelectric coupling and polar nanodomains in the charge-ordered Fe2OBO3 have been extensively studied from room temperature down to 100 K. In situ TEM investigations demonstrate that the charge-ordering transition characterized by an incommensurate modulation could evidently result in remarkable polar nanodomains at low temperatures. This kind of nanodomain could play a critical role in triggering a high dielectric constant and notable dielectric dispersion as observed in Fe2OBO3. Moreover, measurements of the magnetoelectric coupling under electrical field demonstrate the existence of giant electrically induced changes in magnetization around the magnetic transition.