The sonnet opens with a sigh and a complaint: "Ah! wherefore with infection should he live". The speaker cannot understand why a beautiful young man must go on existing in a world he sees as diseased. His presence seems to do harm as well as suffer it, because by "grace[ing] impiety" he lends sin a respectable face, so that wickedness can "lace itself with his society". The poem is about him in the third person, as though the speaker were muttering to the universe rather than to the young man himself. Only at the end do we learn that the complaint is really praise.
The form helps the trick work. This is a Shakespearean sonnet in iambic pentameter, with three quatrains rhyming abab cdcd efef and a closing couplet. Nearly the whole poem is built from questions. "Wherefore" in line 1 becomes "Why should" in lines 5, 7 and 9, and the repetition sounds like an argument that keeps coming back to the same grievance. Each quatrain is one long sentence, so the indignation never has room to cool. Even the rhymes carry meaning. "Impiety" is paired with "society," so moral failure and social life are bound together before we have thought about it. To modern ears "live" and "achieve" in the first quatrain barely rhyme at all, which gives the opening a slightly rough edge, though the sound may have been closer in Shakespeare's day.
The second quatrain moves from sin to cosmetics. "False painting" tries to "imitate his cheek," and the phrase "dead seeming of his living hue" sets lifelessness against life in a single line. The painted face is only a "seeming," while his colour is real. "Poor beauty" has to "indirectly seek / Roses of shadow." A shadow is a mere imitation, and "indirectly" hints at something sneaky, as if the whole business of making oneself beautiful has become a kind of fraud. The answer comes in a short, flat statement: "his rose is true." The rose was already a conventional image of beauty, but here it is used to separate the genuine from the fake.
In the third quatrain the imagery changes from art to money. Nature is "bankrupt," "Beggar'd of blood to blush through lively veins." The image is a clever one, because blushing is the body's own colour, the opposite of rouge, and Nature has run out of it. She has "no exchequer now but his," which makes the young man her only treasury, and she "lives upon his gains" like someone surviving on a single remaining investment. The phrase "proud of many" suggests that she once had plenty to be proud of. Beauty is treated almost as a national economy that has collapsed, with one account left open.
That is why the couplet changes the poem's meaning. After twelve lines that seem to pity him for living among corruption, the speaker reveals what is happening: "O! him she stores, to show what wealth she had / In days long since, before these last so bad." Nature keeps him the way a museum keeps its finest piece, as evidence of how rich the past was. The questions were never really asking him to leave the world. They were asking why the world has fallen so far below him. The word "stores" also suggests that he is being preserved, which adds a faint note of worry about whether something so rare can last. The last line looks back with nostalgia to "days long since," a golden age against a "last so bad" present, and the sonnet's praise turns into a judgment on the age as well.
The poem is significant because it turns flattery into something more interesting. A simple compliment would say that the young man is beautiful. This sonnet makes his beauty a measure of everything around him, so that the more it shines, the worse the surroundings look. It also gives beauty a moral weight, since the real rose, the true blush and the living hue are set against paint, shadow and pretence. The commercial language of exchequer, bankruptcy and gains makes the argument feel startlingly modern.