Background <p>Microsurgical competence is critical for neurosurgery, yet optimal instructional strategies for undergraduate training remain underexplored. This prospective non-randomized historical cohort study compared two instructional strategies in undergraduate microsurgical anatomy education and their effects on learners’ microsurgical competence.</p> Methods <p>Two consecutive cohorts of third-year medical students (<i>n</i> = 20 each) underwent an 8-week microsurgical training program. The 2022 cohort received a conventional theory-first sequential approach, while the 2023 cohort received an integrated theory–practice model. Outcomes were assessed using the MSLQ (Motivated Strategies for Learning Questionnaire), CEQ (Course Experience Questionnaire), SDLRS (Self-Directed Learning Readiness Scale), practical skill checklists, and written examinations. Data were analyzed using paired t-tests, independent-sample t-tests, Wilcoxon test, Mann-Whitney U test and ANCOVA (Analysis of Covariance) with baseline scores as covariates.</p> Results <p>In this prospective cohort study, the integrated theory–practice instructional model was associated with superior microsurgical skill performance, conceptual understanding, learning motivation, and self-directed learning readiness compared with the conventional sequential model. Both approaches significantly improved students’ technical skills. Given the non-randomized design, these findings should be interpreted as preliminary and hypothesis-generating.</p> Conclusions <p>These findings suggest that integrated instructional models may be beneficial in undergraduate microsurgical anatomy training. Further randomized controlled studies are needed to confirm the causal effect of integrated instructional models on microsurgical education outcomes.</p>