The executive branch exercises the most important means of checking Congress: veto power. A presidential veto requires a 2/3rd vote in both chambers of Congress to override. Another way of hemming Congress is the 10th Amendment (Reservation Clause). The 10th Amendment states that power no delegated to the federal government and not prohibited, are reserved only for states or people. A third way of checking Congress is through the judicial branch -- the Supreme Court. Judicial review prevents Congress from passing laws that are unconstitutional.
Judicial review occurs when a person challenges the constitutionality of a law they claim has harmed them. The Supreme Court determines whether a law is constitutional or unconstitutional for the entire nation. For example, when the Supreme Court deemed flag burning legal, all 48 states with laws against flag burning suddenly had no legal basis for this prohibition.
While Congress was given tremendous power, it was kept in check by the executive and judicial branches, states and even its own bicameral structure. This buffeted Congress in various ways. However, the founders did not predict that Congress would allocate power to the executive branch.