In order to solve the problem of city residents live and heavy traffic, the underground engineering construction have entered a rapid development period in the city of southeast coastal regions. The excavation depth of high rise building pit is more and more, the pit is a kind of common construction method in the node projects construction of the subway, and the pit presents a multilayer development trend. However, muddy soft soil of the Holocene is widely distributed in coastal area. Because the properties of soft soil is poor, the construction of pit is very difficult, it is easy to occur some engineering geological problems, such as instability of pit slope, bursting mud and water and the failure of supporting structure, etc. Which bring out some adverse environmental effects, such as ground subsidence, uneven settlement, buildings cracking and damage around the pit. Some engineering geological problems and adverse environmental effects in deep pit construction had intensively been studied in soft soil area, the main factors of affecting foundation pit safety had been analyzed, and the specific prevention measures had put forward in this paper. The prevention measures is successful by the verification of construction of practical foundation pit in soft soil area.