Poor crop establishment of direct-seeded rice (DSR) is one of the major constraints to wide adoption of DSR, particularly in areas prone to flooding after sowing or where fields are not level. Seed pelleting is an effective, practical and facile technique to enhance crop establishment under unfavorable environmental conditions. To evaluate the effects of seed pelleting on rice germination, seedling growth and associated metabolic events under waterlogging stress, various seed pelleting treatments including formulae, pelleting times (the weight ratio of pelleting agents: rice seeds = 1:1~7:1 (w/w) and CaO2 contents were tested in series of experiments. Naked seeds were maintained for comparison as a control. Pelleting treatments with CaO2 significantly increased seed germination and seedling growth of DSR under waterlogging conditions compared with pelleted seeds without CaO2 and naked seeds. The optimum weight ratios of CaO2 to dry seeds were found to be in the range of 0.6:1-1:1 based on seed germination and seedling growth performance under waterlogging conditions. Under waterlogging conditions, high seed germination percentage and vigorous seedling growth of DSR due to seed pelleting with CaO2 was associated with an increase in α-amylase activity, but decrease in alcohol dehydrogenase (ADH) and pyruvate decarboxylase (PDC) activities in pelleted seeds.