Metaphysics are key to the arguments and theories explored in this novel, so for a basic guide I'd go to the ever helpful Wikipedia article.
A lot of the novel's themes of free will, space & time, and matter are all metaphysical concerns and there are many philosophers on which Pullman clearly draws. Interestingly, in the sub-article on free will, one of the main philosophers is Baruch Spinoza. The character Baruch has gone from a human (with free will) to an angel (supposedly without free will), drawing yet another interesting link in Pullman's character names.
Here's a great video that explains metaphysics - a reading from Gerardus Tros: