Here, we demonstrated the optimum design of pillar microstructure for efficient microdroplet merging. The microfluidic device mainly consisted of programmable microvalves and pillar microstructures. Based on the system, aqueous droplets were continuously generated at T-junction using actuating of integrated programmable microvalaves under the immiscible continuous fluid (mineral oil containing 0.5 wt% Span 80). The principle of merging process depended on the competitive correlation of hydraulic pressure of continuous phase and Laplace pressure of the droplet. We found that the design of the micropillars controls above two pressures. Finally, it was demonstrated that the microfluidic system could be able to efficient biochemical reaction. We expect that the microfluidic system is useful analytical or reaction tools in fundamental science, biotechnology, and chemical engineering.