We propose a new compiler framework that automates code generation over multiple fully homomorphic encryption (FHE) schemes. While it was recently shown that algorithms combining multiple FHE schemes (e.g., CKKS and TFHE) achieve high execution efficiency and task utility at the same time, developing fast cross-scheme FHE algorithms for real-world applications generally require heavy hand-tuned optimizations by cryptographic experts, resulting in either high usability costs or low computational efficiency. To solve the usability and efficiency dilemma, we design and implement HEIR, a compiler framework based on multi-level intermediate representation (IR). To achieve cross-scheme compilation of efficient FHE circuits, we develop a two-stage code-lowering structure based on our custom IR dialects. First, the plaintext program along with the associated data types are converted into FHE-friendly dialects in the transformation stage. Then, in the optimization stage, we apply FHE-specific optimizations to lower the transformed dialect into our bottom-level FHE library operators. In the experiment, we implement the entire software stack for HEIR, and demonstrate that complex endto-end programs, such as homomorphic K-Means clustering and homomorphic data aggregation in databases, can easily be compiled to run 72-179× faster than the program generated by the state-of-the-art FHE compilers.