O rose thou art sick (1)
Roses are often symbols of love, but in this poem our symbol is feeling a little under the weather. It's almost as if love is sick as well; this makes sense when we consider that later in the poem, love is "dark and secret" and performs an act of destruction.
Has found out they bed Of crimson joy (5-6)
These lines describe something that is a "joy" to the rose, but we're not really sure what it is. The phrase "crimson joy" reminds us of intense passion—maybe love, seeing as how we've been talking about roses. The fact that the worm discovers it suggests something about tarnishing or corrupting what are supposed to be good things, like love.
And his dark secret love Does thy life destroy (7-8)
The worm's love is "dark and secret"; there is something dangerous about it. What does it mean for love to be "dark" anyway, or secret for that matter? Whatever is "dark" and "secret," even if it's love, is here equated with destruction.