Control structures in Java are essential programming constructs that dictate the flow of execution within a program. They enable developers to make decisions, repeat actions, and manage the sequence of operations based on specific conditions. The primary types of control structures include conditional statements, such as if-else statements, which allow for decision-making; loops, such as for and while loops, which facilitate repetitive tasks; and sequence structures that execute statements in a linear order. Mastering these control structures is crucial for writing efficient, maintainable, and effective Java programs, as they provide the flexibility needed to handle various input scenarios and program logic.