The dominant metaphor here is of a garden, or flower-bed, as representing life, or perhaps a family (it’s a little unclear); only complication is that Taylor calls a garden a “knot.”
Struggles one faces in life, then, are “hellish breath”s, etc. Children are new flowers growing from the stem. “Crop this flower” suggests one child died. Sign that Christ loves your child and wants him or her…. Things get better when more children are born, and then one gets sick as an infant and dies after six weeks of suffering, maybe.
Really, in spite of the metaphor or conceit, this is another poem about viewing your life, and what transpires, of where you stand in God’s estimation, familiar from all the Puritan writers…. There is also the element of consolation, of trying to make sense of tragedy and to find reasons to not mourn so much.
The poem closes with a restatement of this theme: that we all live in God’s hands, that we are his creation, and we should accept that he will dispose of us as he will.