Objective: To investigate the application effects of intelligent guidance systems in optimizing health check-up process management. Methods: A total of 400 examinees who underwent physical examinations at the hospital’s Health Management Center from January to December 2024 were randomly divided into a control group (200 cases) and an observation group (200 cases). The control group used traditional manual guidance methods, while the observation group employed the intelligent guidance system. The study compared two groups in terms of completion time, waiting time for each procedure, check-up efficiency scores, examinee satisfaction, and report issuance time. Results: The overall examination time in the observation group (85.3 ± 12.7 minutes) was significantly shorter than that in the control group (142.6 ± 18.5 minutes) (P < 0.01); average waiting time per procedure decreased by 62.4%; check-up efficiency scores (8.9 ± 0.8 points) were significantly higher than those in the control group (5.2 ± 1.1 points) (P < 0.01); satisfaction reached 96.5%, significantly higher than the control group’s 78.0% (P < 0.01); and report issuance time was advanced by 1.5 days. Conclusion: Intelligent guidance systems can significantly optimize check-up processes, improve work efficiency, and examinee satisfaction, demonstrating significant clinical application value.