Large language models (LLMs) have achieved significant leadership in many NLP tasks, but aligning structured output with generative models in information extraction (IE) tasks remains a challenge. Prompt Engineering (PE) is renowned for improving IE performance through prompt modifications. However, the realm of the sample design for downstream fine-tuning, crucial for task-specific LLM adaptation, is largely unexplored. This paper introduces **Sample Design Engineering** (SDE), a methodical approach to enhancing LLMs’ post-tuning performance on IE tasks by refining input, output, and reasoning designs. Through extensive ID and OOD experiments across six LLMs, we first assess the impact of various design options on IE performance, revealing several intriguing patterns. Based on these insights, we then propose an integrated SDE strategy and validate its consistent superiority over heuristic sample designs on three complex IE tasks with four additional LLMs, demonstrating the generality of our method. Additionally, analyses of LLMs’ inherent prompt/output perplexity, zero-shot, and ICL abilities illustrate that good PE strategies may not always translate to good SDE strategies.