This paper analyses the characteristics of natural runoff annual variability and the concerned influencing factors in Beijiang River Basin in recent 45 years. It is showed that annual variability of natural runoff has phase characteristics in the river, which has an obvious changing after 1984 that continuing low water and high water periods have become longer. It has 21a and 11a period. Rainstorm caused by frontal surface with low trough is the main causation that natural runoff rise quickly. The mountains of Daluo and Shikengkong are two steps of windward slopes, the rainstorm's center that caused by the two windward slopes is the main source of natural runoff in Beijiang River. Natural runoff rises at large after a year when El Nino appears, and in the year when La Nina appears natural runoff rises too. Changing rapidly of Sunspots has changed the system of the earth energy and influenced circulation of atmosphere, which is a main reason that sunspots impact on natural runoff in the Beijiang River Basin.