The invention provides a method for improving the hybrid seed production efficiency and increasing the yield of hot pepper. The method comprises the following steps: adjusting the sowing time, reasonably performing dense planting in a facility, adjusting plants, collecting pollen, emasculating and pollinating, performing plant management after pollination, harvesting seeds and the like. Through covering with nylon gauze in the facility for isolated breeding, the purities of parents are guaranteed to meet original seed requirements; through adjustment of the sowing time, the most suitable climatic condition is provided for flower synchronization of the male and female parents and the pollination; through reasonable dense planting in the facility, a suitable microclimate environment can be created for hot pepper seed production, and the planting density and the planting ratio of the male and female parents are determined according to the parental plant height and pollen collecting requirements; through improvement on a method for collecting pollen of the male parents, the pollen amount and the pollen quality are guaranteed; emasculation, pollination and labeling are completed in onetime, so that repeated pollination is not needed, the labor is reduced, and the seed production efficiency is improved; through plant management after the pollination, the seed setting rate is also improved; the problems that in the prior art, the efficiency is low, the yield is not high and the purity is unstable in the hybrid seed production process of the hot pepper are solved.