In the first stanza, the speaker compares the lady "like the night / Of cloudless climes and starry skies." The lady is a combination of the best of "dark and bright." Therefore, she is the best of both worlds: night and day. This is not just her outward appearance but also her inward beauty. This is subtly indicated by the mention of her eyes which are windows to the soul.
In the second stanza, we have more combinations of dark and light. The speaker suggests that this lady has the perfect balance of these opposites. If she were to have a bit more dark or a bit less light, she would be not as striking ("half impair'd").
One shade the more, one ray the less,
Had half impair'd the nameless grace
Which waves in every raven tress,
Or softly lightens o'er her face;
She is beautiful but she's also graceful and her beauty (evidenced by her perfect balance of dark and light) shows her inward beauty: her "thoughts serenely sweet" are expressed by that external beauty.
In the third stanza, the speaker notes how the lady's physical beauty tells "of days in goodness spent" and this shows another balance. Her external beauty corresponds to her internal goodness.
In this respect, the poem is about harmonies and balance. Although the speaker seems to be praising the lady's outwardly beautiful balance of dark and light, he's also praising her inner beauty. The lady is therefore beautiful, "at peace", and has an innocent heart. She is the perfect balance of dark and light, internal and external beauty/goodness.