The management of elites, as one of the pillars of sustainable development and a knowledge-based economy, faces numerous challenges in Iran. The main issue of this research is to identify these challenges and propose solutions to improve the management of elites. The primary research question examines the factors affecting the decrease in the motivation of elites and the increase in their migration. This study was conducted using a mixed-methods approach, incorporating qualitative data from 25 experts and quantitative data from 350 active elites in scientific and industrial fields. The results indicate that challenges such as administrative corruption, lack of transparency, social barriers, and weak research infrastructure contribute to the decline in the motivation of elites. Additionally, the average motivation for elites to remain is significantly below the average level (2.8 out of 5), with management challenges (average 4.2 out of 5) identified as the most significant barrier. Based on the findings, suggestions such as transparency in policymaking and the development of research infrastructure have been proposed. This research demonstrates that the adoption of effective policies can lead to a reduction in the migration of elites and better utilization of human capacities.