Large language models (LLMs) have demonstrated impressive performance in code generation, particularly when augmented with chain-of-thought (CoT) prompting techniques. They break down requirements into intermediate reasoning steps, which act as design rationales to guide LLMs in writing code like human programmers. Thus, the quality of these steps is crucial for ensuring the correctness and reliability of the generated code. However, little is known about the quality of CoT generated by LLMs. To what extent can we trust the thoughts generated by LLMs? How good are they? This paper empirically explores the external and internal factors of why LLMs generate unsatisfactory CoTs by analyzing 1,023 failed code samples on two widely used code generation benchmarks. We also evaluate their impact on code generation performance by analyzing 210 CoT-code pairs and refining the unsatisfied CoTs by prompting LLMs. Our study reveals three key findings: (1) External factors (53.60%), such as unclear requirements and lack of context, mainly affect CoT quality, while internal factors (40.10%) stem from LLMs' misunderstanding prompts. (2) Even when CoTs are correct, 18.5% of the generated code contains errors due to instruction-following issues; conversely, 11.90% of correct code is paired with flawed CoTs. (3) Refining low-quality CoTs is feasible, i.e., LLMs improve when given detailed problem descriptions. These findings highlight key challenges in CoT-based code generation and suggest directions for improving LLM reasoning and reliability.