Legal Judgment Prediction (LJP) aims to form legal judgments based on the criminal fact description. However, researchers struggle to classify confusing criminal cases, such as robbery and theft, which requires LJP models to distinguish the nuances between similar crimes. Existing methods usually design handcrafted features to pick up necessary semantic legal clues to make more accurate legal judgment predictions. In this paper, we propose a Semantic-Aware Dual Encoder Model (SEMDR), which designs a novel legal clue tracing mechanism to conduct fine-grained semantic reasoning between criminal facts and instruments. Our legal clue tracing mechanism is built from three reasoning levels: 1) Lexicon-Tracing, which aims to extract criminal facts from criminal descriptions; 2) Sentence Representation Learning, which contrastively trains language models to better represent confusing criminal facts; 3) Multi-Fact Reasoning, which builds a reasons graph to propagate semantic clues among fact nodes to capture the subtle difference among criminal facts. Our legal clue tracing mechanism helps SEMDR achieve state-of-the-art on the CAIL2018 dataset and shows its advance in few-shot scenarios. Our experiments show that SEMDR has a strong ability to learn more uniform and distinguished representations for criminal facts, which helps to make more accurate predictions on confusing criminal cases and reduces the model uncertainty during making judgments. All codes will be released via GitHub.