By using the daily precipitation data of 66 stations in Fujian and NCEP reanalysis data and OLR data during 1979-2010, this paper reveals the low frequency features of precipitation during pre flood season in Fujian and analyzes the atmospheric low frequency oscillation (LFO) features during persistent heavy rain processes and the evolution characters of the previous LFO signs. The results indicate that the daily precipitation during pre flood season of Fujian has significant features of LFO. The main low frequent periods are 10-20 d, 30-60 d and 20-30 d respectively. More than two kinds of significant cycle periods are found with proportion of about 63%. The proportion of variance contribution of 10-90 d reaches 20%-30%. The correlations between the total rainfall in pre flood season and the intensity of LFO are significantly positive, and the intensity and the duration of persistent heavy rains are closely related to the features of rainfall LFO. In the years when precipitation is mainly controlled by BWO (ISO), the duration of persistent heavy rains is shorter (longer). In addition, during the persistent heavy rain weathers, there are anticyclones over the sea area to the east of Japan, the east of Somali and the South China Sea, which cause cold flows from Japan down to Bohai Bay to encounter the two cross equatorial flows from Somali and South China Sea over Fujian, and then low frequency cyclones are formed there resulting in the low frequency convergence in the lower level and divergence in the upper level and the convection enhanced. Moreover, the persistent heavy rain in Fujian is closely related to the variations of tropical and subtropical atmospheric LFO. The eastward propagation of tropical Madden Julian Oscillation (MJO) and northward propagation of East Asia Pacific ISO have denotative significance for extended range forecast.