There are a number of limitations that have been placed on the power of the Supreme Court by the Constitution.
First, the members of the Supreme Court are liable to impeachement. They are allowed to continue in office during "good behavior," which means that Congress can impeach them.
Second, Congress has the power to set the jurisdiction of the Court (at least in issues of statutary law). In other words, Congress can tell the Court to some extent what sorts of cases it may and may not hear.
The most important limitation on the power of the Court is one that is not explicitly stated in the Constitution. That is the fact that the Court has no means of executing its decisions. It has no police force that it can send out to force people to obey. It has to rely on the executive branch to enforce decisions it has made.
checks and balances