By “the work of male and female”, Milton means procreation (the generation of children), and by association, sexual intercourse. In this passage Milton explains that an advocate of divorce must expect two sources of objection: the first based on the solemnity of the marriage vow, and the second based on the “gross and vulgar apprehension” that the only purpose of marriage is the begetting of children, and so the suitability of the married couple is irrelevant. Compare 1.13, where Milton writes:
I suppose it will be allowed us that marriage is a human Society, and that all human society must proceed from the mind rather then the body, else it would be but a kind of animal or beastish meeting; if the mind therfore cannot have that due company by marriage, that it may reasonably and humanly desire, that marriage can be no human society, but a certain formality; or gilding over of little better then a brutish congress, and so in very wisdom and pureness to be dissolved.
John Milton (1643). The Doctrine and Discipline of Divorce, book 1, chapter 13. In The Works of John Milton, volume 3, part 2, pp. 422–423. Columbia University Press. Spelling modernized.
The phrase is also found in the work of Milton’s contemporary, the anatomist William Harvey, where the context makes it a bit clearer that the meaning is “procreation”:
God, Nature, or the Soul of the universe, […] by his deity or providence, his art and mind divine, engenders all things, whether they arise spontaneously without any adequate efficient,† or are the work of male and female associated together,‡ or of a single sex, or of other intermediate instruments, here more numerous, there fewer, whether they be univocal, or are equivocally or accidentally produced: all natural bodies are both the work and the instruments of that Supreme Good, some of them being mere natural bodies, such as heat, spirit, air, the temperature of the air, matters in putrefaction, &c., or they are at once natural and animated bodies; for he also makes use of the motions, or forces, or vital principles of animals in some certain way, to the perfection of the universe and the procreation of the several kinds of animated beings.
William Harvey (1651). Anatomical Exercises on the Generation of Animals, exercise 50. Translated by Robert Willis (1847). In The Works of William Harvey, p. 370. London: Sydenham Society.
† Here “efficent” means “cause” (OED sense B.1). ‡ Harvey’s original Latin is “maris fœminæque simul sociatis operis”. See Exercitationes de generatione animalium, pp. 146–147.