The speaker of the poem is attempting to persuade a woman to have sex with him. She responds by squashing a flea. The speaker then goes on to create an analogy of the, the woman and the flea to support his argument. The speaker says that since the flea bit and sucked each them, their blood is already intermingled, so they have already exchanged bodily fluids; an obvious reference to sexual intercourse. “three lives in one flea spare/where we almost, yea, more than married are.” He urges her not to kill the flea (“stay”) because it will kill her and the speaker because their blood is mixed in the flea. She kills the flea, but the speaker has one last resort. He says that he and she are not ‘the weaker’ after the death of the flea and that she will only lose a little honor in yielding to his request.
The analogy with the man, woman and flea is a metaphysical conceit; an extended analogy that requires more explication than simpler analogies.