Water temperature in the eastern part of the Yellow Sea (EYS) during winter (JFM) and summer (JJA) from 1964 to 2009 and Siberian High Pressure Index (SHI) and Arctic Oscillation index (AOI) during winter (JFM) from 1950 to 2011 were used to analyze long-term variation in oceanic and atmospheric conditions and relationship between winter and summer bottom water temperature. Winter water temperature at 0, 30 and 50 m had fluctuated highly till the late of 1980s, but after this it was relatively stable. The long-term trends in winter water temperature at both depths were separated with cold regime and warm regime on the basis of the late 1980s. Winter water temperature at 0m and 50m during warm regime increased about $0.9^{circ}C$ and $1.1^{circ}C$ respectively compared to that during cold regime. Fluctuation pattern in winter water temperature matched well with SHI and AOI The SHI had negative correlation with water temperature at 0 m (r=-0.51) and 50 m (r=-0.58). On the other hand, the AO had positive correlation with Winter water temperature at 0 m (r=0.34) and 50 m (r=0.45). Cyclic fluctuation pattern of winter water temperature had a relation with SHI and AO, in particular two to six-year periodicity were dominant from the early of the 1970s to the early of the 1980s. Before the late of 1980s, change pattern in winter water temperature at 0 and 50 m was similar with that in the bottom water temperature during summer, but after this, relationship between two variables was low.