Congress participates in checks and balances by regulating the behaviors of the executive branch.
For example, if Congress passes a bill the executive branch has the chance to review it before it becomes law. If the president, who is part of the executive branch, decides to veto the bill then Congress can use their power to check the power of the executive branch. Congress can do this by overriding the veto. This would take a 2/3 vote in both the Senate and House of Representatives.