This song epitomises what it means to be in love. The entire song points out that no matter what, he'll never see flaws with the girl that she loves - that is, her 'perfect imperfections' - as to him, he knows that he'll be in love with her no matter what.
That no matter what happens, how she's feeling or what she's doing, that he'll always be there and always see her in the best possible light.