Congress is checked by the Supreme Court through the power of judicial review.
Judicial review is a power that the Supreme Court possesses thanks to the Marbury vs. Madison case. Judicial review allows the Supreme Court to rule on whether laws made by Congress are constitutional or unconstitutional. Any law passed by Congress that the Supreme Court thinks violates the US Constitution immediately becomes void. This ensures that the Supreme Court can get rid of any law made by Congress that may violate a citizens rights.