Code generation remains a challenging task that requires precise and structured reasoning. Existing Test Time Scaling (TTS) methods, including structured tree search, have made progress in exploring reasoning paths but still face two major challenges: (1) underthinking, where reasoning chains tend to be shallow and fail to capture the full complexity of problems; and (2) overthinking, where overly verbose reasoning leads to inefficiency and increased computational costs. To address these issues, we propose LogitsCoder, a novel framework that enhances chain-of-thought reasoning through lightweight, logit-level control mechanisms for code generation. LogitsCoder iteratively generates and refines reasoning steps by first steering token selection toward statistically preferred patterns via Logits Preference Decoding, then selecting and aggregating diverse reasoning paths using Logits Rank Based Path Selection and Thoughts Aggregation. This results in coherent and effective reasoning chains that balance depth and efficiency. Extensive experiments demonstrate that LogitsCoder produces more efficient and higher-quality reasoning chains, leading to superior code generation performance compared to baseline methods.