The hydrogen bonds in films of the polyurethane and the core-shell type polyacrylate-polyurethane microemulsions have been studied by FTIR spectroscopy in the regions of-NH absorption and C=O absorption. The effects on hydrogen bonds of the composition, the core-shell ratio were revealed. At the same time, the relationship between the hydrogen bonds and the crosslinked structures (Type A and Type B) was discovered. The shifts of the -NH and C=O stretching bands to higher frequencies and the shift of -NH bending bands to lower frequencies, with the increase of acetone C=O number in the core, mean that the hydrogen bonds between the soft and hard segments, and those in the short-range order in the hard segment phase, are broken. The dipole/dipole interaction which is supposed to exist between the acetone C=O groups in the core and the urethane C=O in the shell can change the hydrogen bond distribution in the shell, and at the same time, lead to hydrogen bonds between acetone C=O in the core and the urethane -NH in the shell. Type A and B crosslinked structure between the core and the shell located at the interface of the core and the shell can confine the acetone C=O within the crosslinking network, and Type B crosslinked structure also decreases the acetone C=O numbers. These weaken the dipole/dipole interaction between the acetone C=O and the urethane C=O, and lead to the decrease of the effect of the acetone C=O groups on the hydrogen bond distribution in the shell.