The rapid advancements of AI rely on the support of integrated circuits (ICs). However, the growing complexity of digital ICs makes the traditional IC design process costly and time-consuming. In recent years, AI-assisted IC design methods have demonstrated great potential, but most methods are task-specific or focus solely on the circuit structure in graph format, overlooking other circuit modalities with rich functional information. In this paper, we introduce CircuitFusion, the first multimodal and implementation-aware circuit encoder. It encodes circuits into general representations that support different downstream circuit design tasks. To learn from circuits, we propose to fuse three circuit modalities: hardware code, structural graph, and functionality summary. More importantly, we identify four unique properties of circuits: parallel execution, functional equivalent transformation, multiple design stages, and circuit reusability. Based on these properties, we propose new strategies for both the development and application of CircuitFusion: 1) During circuit preprocessing, utilizing the parallel nature of circuits, we split each circuit into multiple sub-circuits based on sequential-element boundaries, each sub-circuit in three modalities. It enables fine-grained encoding at the sub-circuit level. 2) During CircuitFusion pre-training, we introduce three self-supervised tasks that utilize equivalent transformations both within and across modalities. We further utilize the multi-stage property of circuits to align representation with ultimate circuit implementation. 3) When applying CircuitFusion to downstream tasks, we propose a new retrieval-augmented inference method, which retrieves similar known circuits as a reference for predictions. It improves fine-tuning performance and even enables zero-shot inference. Evaluated on five different circuit design tasks, CircuitFusion consistently outperforms the state-of-the-art supervised method specifically developed for every single task, demonstrating its generalizability and ability to learn circuits' inherent properties.