Juvenile flower ginseng Stichopus monotuberculatus are highly sensitive to environmental changes and anthropogenic stimuli, resulting in significant stress and high mortality during transportation of hatchery-reared juveniles. Developing an effective anesthetic method can alleviate stress responses and reduce mortality during transport. This study compared the anesthetic effects of five commonly used aquatic anesthetics, i.e., clove oil, 2-phenoxyethanol, magnesium sulfate, MS-222, and magnesium chloride, on juvenile Stichopus monotuberculatus. A behavior-based evaluation method for anesthetic and recovery stages was established, dividing the entire process into six phases: light anesthesia, moderate anesthesia, deep anesthesia, light recovery, moderate recovery, and full recovery. The results showed that clove oil, magnesium sulfate, and magnesium chloride effectively anesthetized juvenile Stichopus monotuberculatus. Clove oil at a concentration of 0.2 mL/L exhibited the best anesthetic effect, whereas concentrations of 0.02 mL/L and 0.04 mL/L significantly improved survival rates during prolonged transportation. Clove oil at 0.5 mL/L induced the shortest anesthesia duration of (6.04±1.24 min). Using magnesium sulfate at 0.05 mol/L resulted in the slowest time to achieve deep anesthesia [(34.13±3.77) min], while magnesium chloride at 0.05 mol/L produced the fastest full recovery of (10.01±1.36) min and magnesium sulfate at 0.25 mol/L produced the slowest time to full recovery [(60.39±5.28) min]. High concentrations of magnesium chloride and magnesium sulfate caused no significant changes in the body length of juvenile Stichopus monotuberculatus before and after anesthesia, whereas MS-222 and 2-phenoxyethanol were ineffective as anesthetics. This study identified clove oil at a concentration of 0.02 mL/L as the most suitable anesthetic for juvenile Stichopus monotuberculatus, ensuring effective recovery and high survival rates after 60 hours of long-distance transport. These findings provide critical technical support for the safe transportation of juvenile Stichopus monotuberculatus over long distances.