By using the 1994-2010 observation data of paddy rice growth period and yield from 14 agro-meteorological stations at different altitudes in Yunnan Province, this paper studied the rice yield formation and the effects of meteorological factors on low-yield rice yield components. According to the systematic cluster analysis of rice yield components and the rice types at the 14 stations, the rice was divided into 4 types, i. e., low-yield japonica rice, low-yield indica rice, high-yield japonica rice, and high-yield indica rice. The analysis of the yield components of the 4 rice types showed that there was a significant positive correlation between the spikelet number per square meter (sqm) and the rice yield. The yield of low-yield japonica was mainly affected by the seed setting rate and the spikelet number per sqm. For the other three rice types, the spikelet number per sqm had greater effects on the rice yield. The low-yield japonica rice was mainly affected by low temperature. At booting stage, low temperature decreased the spikelet number and the productive panicle number of unit sqm. At booting and flowering stages, low temperature increased the empty grain rate, and the effects of average temperature, average maximum temperature, and cold accumulated temperature were greater. At pre-milk stage, low temperature increased the unfilled grain rate, and meanwhile, decreased the 1000-grain mass. The yield components of low-yield indica rice were obviously affected by multiple meteorological factors. A certain degree of warming at tillering and jointing stages was not beneficial to the increase of productive panicle number per sqm of low-yield indica rice, but the more sunshine hours and the greater average diurnal temperature range at tillering stage was beneficial to the increase of the productive panicle number per sqm. There was a parabolic relationship between the temperature and sunshine hours at tillering and jointing stages and the spikelet number per panicle. The low temperature at flowering stage affected the empty grain rate of low-yield indica rice to a certain extent, while the high temperature and less rain at pre-milk stage not only increased the unfilled grain rate, but also distinctly reduced the 1000-grain mass.