Donne and Marvell, born in 1572 and 1621 respectively, lived about 100 years apart. There will be some interesting differences between their poems, especially in terms of tone and thematic emphasis. The metaphysical movement was a loose impulse of the 17th century affecting poets who usually didn't know each other (as Donne and Marvell) or read each other's poems; it lasted a good century before waning. Compare this to the active collaboration between Romantic poets Wordsworth and Coleridge and between Keats and Shelly.
On personal differences between them, Donne, a Catholic during a period of active Catholic persecution and massacre, was coerced to convert to Anglican Protestantism after his brother died in prison for failing to swear allegiance to the Thirty-one Articles of Anglicanism. On the other hand, Marvell was an Anglican Protestant who served in Cromwell's Protestant Interregnum government following the English Civil Wars that led to King Charles I's beheading. Coming from such opposite backgrounds and living through such different times naturally results in differences in personal expression and thematic interests.
For instance, in his Pseudo-Martyr collection (1610), Donne took on the subject of the laws of the Church and defended a Catholic's loyalty to the Crown in light of those laws. As a result, James I decreed that Donne might be employed in no occupation other than as an Anglican clergyman, thus forcing Donne to become a Protestant minister. In contrast, Marvell published little during his lifetime and his greatest lyric poems are thought to have been written early in his career while he was a tutor and before he was Milton's Latin secretary. His most famous works were published posthumously (after his death).
To illustrate the differences in tone and thematic emphasis, we'll consider Donne's "Lovers' Infiniteness" and Marvell's "The Definition of Love." The subject is the same, but will their tones and approach to the theme be?
Donne's metaphysical conceit is a comparison of love to marketing and business: my treasure, bargain, stocks, letters, outbid. Marvell's metaphysical conceit is harder to pin down being fugue-like. It starts with implied comparisons to human states of being (e.g., "Magnanimous Despair") through the personifications of emotion, love and fate, then, at stanza 5, it swings to a comparison of love to physical properties in the world: world wheels about, planisphere, parallel, conjunction, opposition of stars.
Donne's tone is ponderous, serious, as it labors through elaborate arguments:
Or if then thou gavest me all,
All was but all, which thou hadst then;
But if in thy heart, since, there be or shall
New love created be,...
Marvell's tone is light, optimistic, victorious even though thwarted:
Therefore the Love which us doth bind,
But Fate so enviously debars,
Is the conjunction of the Mind,
And opposition of the Stars.
For further differences, you might consider the structure of their various poems, beginning with these two.