Improving the growth and health status of marine fish larvae to adapt to climate change, is crucial for commercial hatchery production in tropical regions. This study evaluated the effects of dietary essential fatty acids used for Artemia enrichment on growth, biochemical responses, skeletal morphology, and stress resistance of Asian sea bass larvae, reared at high temperatures of 30 °C and 34 °C. Starting 11 days after hatch, Asian sea bass larvae, were fed Artemia, enriched with a commercial emulsion of n-3 HUFA for 14 days, at four concentrations (0, 100, 300, and 500 ppm), at two rearing temperatures (30 °C and 34 °C). The results showed that enriching Artemia with n-3 HUFA significantly improved the final weight and specific growth rate of the larvae fed n-3 HUFA enrichment at 300 ppm, at 34 °C (P < 0.05). Moreover, n-3 HUFA enriched Artemia significantly increased the essential fatty acids of the larvae in parallel with the dose of enrichment. Fish fed unenriched HUFA Artemia resulted in significantly higher ratio of skeletal deformities and lower survival rate following an air exposure test than the larvae fed the n-3 HUFA enriched diets. Overall, the findings showed that n-3 HUFA-enriched Artemia diets had benefits on body weight, specific growth rate, and stress tolerance in Asian sea bass fed HUFA enriched diets, even at high temperatures.