Mix dark soy sauce, honey, pepper and 5 spice powder in a bowl and marinate duck thighs in mixture and set aside for 30 minutes.
Grind shallots and garlic until fine. Heat oil in pot until hot and sear the thighs, skin side down until brown, remove and set aside.
Lower heat and add the ground shallots, garlic, star anise, cinnamon and stir fry until fragrant. Pour in half the water and scrape the bottom of pot. Add the soy sauce, sugar and salt. Place thighs in pot, cover and simmer for 10 minutes.
Remove lid and pour in the rest of the water, turn the thighs on the other side and cover and simmer for another 20 minutes until the meat is tender. Let cool and chop the thighs into pieces before serving.