The appropriate timing of mechanical weeding was determined for the control of Monochoria vaginalis, a common and noxious weed in organic paddy fields, with regard to the relationship between root-pulling resistance and leaf stage. The root-pulling resistance increased exponentially with the progression of leaf stage; the resistance increased 2.2-fold at each stage after the 1st leaf stage in both pot and field experiments, showing that leaf stage may be a useful indicator of the appropriate timing of mechanical weeding. The weeding efficiency of a riding-type weeder (“High-Precision Paddy Weeder”) substantially decreased after Monochoria vaginalis plants had grown beyond the 1st leaf stage. Therefore, weeding with this type of weeder should be conducted before the 1st leaf stage. The exponential relationship between root-pulling resistance and leaf stage of Monochoria vaginalis indicates the importance of the timing of mechanical weeding in paddy fields.