Political theory is a subset of political science. Political science studies all areas of politics systematically.
Political theory focuses on the theoretical aspects of philosophy, rather than studying the empirical facts of philosophy. Political theory might therefore explain what a specific form or method of government should be, in a pure or abstract form. You would define what democracy is in theory, what a monarchy is in theory, and so on.
Political theory can also have a normative element: it can explain what a democracy should be, or how citizens should behave in a democracy. It could tell you how a leader should act, or what ethics support a specific political system.
At its most subtle, political theory involves things like how societies form shared knowledge, or how beliefs circulate through a population, and therefore intersects with epistemology.