The Metaphysical Poets were known for their use of extended metaphors (conceits). While some poets associated with this group did address subjects and ideas that we would call metaphysical ("above" the physical) or spiritual, this was not necessarily the case.
But in this poem, Donne does use the extended metaphor and he also mentions metaphysical notions. In this poem, the speaker tells his beloved that she should not mourn his death because their love is at a spiritual (metaphysical) level. The speaker even mocks those whose love is merely earthly, physical, or "sublunary."
Dull sublunary lovers' love
(Whose soul is sense) cannot admit
Absence, because it doth remove
Those things which elemented it.
In other words, anyone who does not understand the soul in the spiritual sense, cannot bear to lose a loved one. If he/she does not understand love in the spiritual sense, he/she will not understand that this kind of love is unaffected by death. This is the general message of the poem. The speaker tells his loved one not to mourn his death because their love is metaphysical/spiritual. Death can not affect it.
He adds that death is not a separation, but an "expansion" of their love. Then, he uses the extended metaphor of two compasses which move in unison. They are inextricably linked. This metaphor parallels their inextricably linked spiritual love. (This linkage also seems like a prescient description of quantum entanglement. This is when two particles are linked and neither time nor space can sever that link.)