This paper has aimed to prevent excessive heat input by controlling arc distribution and heat input capacity with pulse GTAW in order to improve weld quality in 0.08mm pressure gauge diaphragm and flange welding parts. A design of experiment was designed using Box-Behnken method to optimize a welding process. The pulse GTAW parameters such as pulse current, base current, pulse duty, frequency and welding speed were set to input variables while hydraulic pressure that represents welding characteristics in diaphragm and flange joint were set to output variables. Based on the test result, a second regression equation was obtained between input and output variables and turned out significant. Besides, an influence of parameters has been confirmed through response surface analysis using the second-order regression equation and optimum welding condition was obtained through a grid-search method. The optimum welding condition was set to pulse current 84.4(A), base current 29.6(A), pulse duty 58.8(%), frequency 10(%), and welding speed 596(mm/min). Then, decent bead shape was acquired with no excessive heat input under the $2.3kgf/cm^2$ of hydrostatic pressure.