Silicon (Si) is a beneficial element for healthy growth and high and sustainable production of rice, but the mode of action of the beneficial effects has not been well understood. We carried out field trials for four years at two different locations to re-examine the effects of Si on the growth and production of rice using a low silicon rice (lsi1) mutant. The mutant accumulated much lower Si at each growth stage compared with the wild-type rice (Oryza sativa L. cv Oochikara), but there was no difference in the accumulation of other nutrients including N, P, and K. Measurements at different growth stages showed that low Si in the mutant hardly affected the tiller number, chlorophyll content (SPAD value), and root growth. The plant height and shoot dry weight of the wild-type rice were slightly higher than those of the mutant at a later growth stage, but the difference was not significant between the two lines. However, grain yield was reduced by 79–98%, depending on year, due to a low Si accumulation in the mutant, which showed the largest effect of Si on rice production among all studies reported so far. Among the yield components, the percentage of filled spikelets was mostly affected, being only 13.9% of the wild-type rice in the mutant. The grain color of the mutant became brown because of excessive transpiration and infection of pathogens. These results indicate that Si increases rice yield mainly by enhancing the fertility of spikelets.