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Errors in quantum programs are challenging to track down due to the uncertainty of quantum programs. Testing is, therefore, an indispensable method for assuring the quality of quantum software. Existing testing methods focus only on testing quantum programs with quantum circuits or single subroutines and, therefore, cannot effectively test quantum programs with multi-subroutines. In this paper, we first discuss several critical issues that must be considered when testing multi-subroutine quantum programs and point out the limitations and problems with existing testing methods. We then present a novel framework for testing multi-subroutine quantum programs that allow for both unit and integration testing. Our framework includes two novel test coverage criteria for the equivalent class partition of quantum variables to guide our testing tasks and techniques to test quantum programs with several common patterns. We also discuss how to generate test cases based on our framework. To evaluate the effectiveness of our testing framework, we implemented a tool called QSharpTester for testing Q\# programs with multiple subroutines. We used it to conduct experiments on hundreds of mutation programs deriving from seven original Q\# programs. The experimental results show that our testing methods can deal with broader types of quantum programs than existing ones and perform well on almost all faulty mutation programs.