Marine microalgae (
MA
) has received wide attention as a promising source of omega-3 long-chain polyunsaturated fatty acids (
n-3 LC-PUFA
) enrichment in animal products to improve the health status and wellbeing of the consumers. This study evaluated dynamic changes in n-3 LC-PUFA, color, and functional properties as well as atherogenic and thrombogenic health lipid indices of egg yolk from hens fed graded levels (0, 0.5, and 1.0%) of docosahexaenoic acid (
DHA
)–rich MA (
Aurantiochytrium
sp.) during a 56-D feeding period. Egg freshness parameters and yolk lipid oxidative stability were also measured after 0, 14, and 28 D of refrigerated storage. The hen performance and egg quality (except for yolk color) were not affected (
P
> 0.05) by MA supplementation. Docosahexaenoic acid contents in yolk from hens fed 1.0% MA increased quadratically with feeding time with a plateau at about 30 D (
P
< 0.05). Afterward, the DHA content leveled off to a constant value (946.3 mg/100 g yolk) with the n-6/n-3 ratio at 3.5: 1. Dietary inclusion of 1.0% of MA also significantly decreased the atherogenic and thrombogenic indices of yolk lipid (
P
< 0.05). Because the microalgal carotenoids incorporated into egg yolk, the
L
∗ value of yolk from hens fed MA decreased whereas
a
∗ value increased (
P
< 0.05), corresponding to yolk Roche color scores. As expected, there were no significant changes in yolk functional properties (e.g., viscosity and emulsifying activity) related to DHA enrichment (
P
> 0.05). Microalgal carotenoids enrichment also helped attenuate fatty acid oxidation of the DHA-enriched yolk and increase their lipid oxidative stability. In conclusion, dietary supplementation with up to 1.0% of MA significantly increased DHA contents with more health-promoting n-6/n-3 ratio and atherogenic and thrombogenic indices, as well as more intense yolk color within consumers' acceptability, and the feeding strategy had a minimal impact on yolk physical and functional properties or oxidative stability during subsequent refrigerated storage.