This study has been conducted to investigate the thermopneumatic and flow characteristics of diffuser/nozzle based thermopneumatic micropumps. In this study, a transient three-dimensional numerical analysis using FSI (Fluid-Structure Interaction) model has been employed to analyze the effects of the interaction between the membrane and two fluids (air and water) in the thermopneumtic micropump. The transient temperature and pressure in the cavity, the transient displacements of the membrane and the net flow rate of the micropump have been closely calculated for the frequency of 1 Hz. It has been found that the difference of the flow rates at the inlet and outlet is larger in the cooling period than in the heating period and that the duty ratio is very important in association with pump performance because the temperature in the cavity ascends drastically in the heating period and descends slowly in the cooling period. This study can be regarded as fundamental understandings for the design and analysis of thermopneumatic micropumps.