Code transformation is a foundational capability in the software development process, where its effectiveness relies on constructing a high-quality code representation to characterize the input code semantics and guide the transformation. Existing approaches treat code transformation as an end-to-end learning task, leaving the construction of the representation needed for semantic reasoning implicit in model weights or relying on rigid compiler-level abstractions. We present SemRep, a framework that improves code transformation through generative code representation learning. Our key insight is to employ the semantics-preserving transformations as the intermediate representation, which serves as both a generative mid-training task and the guidance for subsequent instruction-specific code transformations. Across general code editing and optimization tasks (e.g., GPU kernel optimization), SemRep outperforms the extensively finetuned baselines with strictly the same training budget by 6.9% in correctness, 1.1x in performance, 13.9% in generalization, and 6.7% in robustness. With the improved exploration of diverse code transformations, SemRep is particularly amenable to evolutionary search. Combined with an evolutionary coding agent, SemRep finds optimizations that 685B larger-weight baselines fail to discover while achieving the same performance with 25% less inference compute.