Sealing of contained fluids is the primary criteria required for pipe flange connections. Recently, there is a rapid rate of increase in the use of low temperature fluids, and leakage related accidents have been reported. Its leakage mechanism seems to be different from the case in pipe flange connections at elevated temperatures. In this paper, it is examined how the leakage of low temperature fluids occurs, in which a pipe flange connection is cooled by liquid nitrogen. The variations of bolt temperature and bolt force are continuously measured. Experimental results show that the bolt force is reduced to as low as about 65% of the initial value. Next, a numerical method based on three-dimensional FEM is proposed to simulate the cooling process. Numerical results are in good agreement with those from experiments. Applying the numerical method to the pipe flange connections for LNG, showed a bolt force reduction of 70% of the initial value. The numerical method proposed in this paper is expected to be applied to cases of different low temperature fluids under various flow conditions.