A self-extending polyester composite yarn with the flat cross sectional POY(Partially Oriented Yarn) and a manufacturing method thereof are provided to impart the over-feed into the flat cross sectional POY, thereby reducing the difference of the dyeing property and enhancing the uniform dyeing property. The polyester flat cross sectional POY has the thickness of mono denier of 0.5 to 2 denier and the total denier of 50 to 120 denier. The polyester flat cross sectional POY is processed under the condition of over-feed of 9 to 25%, the temperature of a hot roller of 95 to 115 degrees in centigrade, the temperature of a hot plate of 150 to 170 degrees in centigrade. The air confounding of the polyester flat cross sectional POY and the polyester SDY is performed so that the self-extending working yarn is manufactured. At the polyester SDY, the thickness of mono denier is 1-10 denier and the total denier of 30-120 denier.
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