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Mechanical transplanting with carpet seedlings (MC) and mechanical direct seeding (MD) are newly developed planting methods, which increase in popularity and planted area each year. Knowing the difference for yield and rice quality under different planting methods is of great importance for the development of high quality and yield cultivation techniques under mechanical conditions. Therefore, three kinds of japonica rice including hybrid japonica rice, inbreed japonica rice, and soft rice were adopted as materials. And the differences in the quality of processing, appearance, cooking and eating quality, nutrition, and the rapid viscosity analyzer (RVA) profile were studied to reveal the effects of planting methods on yield and quality of different types of japonica rice. Results showed that the milled rice and head rice rates under MC was significantly higher than those under MD, and the processing quality of inbreed japonica rice was the most stable. Compared with MC, length/width ratio of rice under MD was significantly increased, and chalkiness rate, size, and degree were significantly decreased. The protein content under MD was lower than that under MC. MC showed higher peak viscosity and breakdown value than MD. The taste value was the greatest for soft rice, followed by inbreed japonica rice, and then by japonica hybrid rice, with no significant differences resulting from planting methods. Compared with MC, MD significantly improved the appearance quality, though processing quality and nutritional quality were decreased. And there was no significant difference in cooking and eating quality between MC and MD. Under different planting methods, the appearance quality of inbreed japonica rice changed the most and the processing quality was the most stable. The nutritional, cooking and eating quality of soft rice changed the least. Therefore, according to the different planting methods and market needs, selecting the appropriate rice varieties can reduce the risks in rice production and achieve good rice quality.