Fill a large pot with about 6 quarts (5 ½ L) of water and add the beef shank, 3 scallions, 5 slices of ginger, and 3 star anise pods. Cover, bring to a boil over high heat, and cook for 5 minutes.
Remove the meat from the pot, rinse in cold water, and cut into thick slices. Discard the cooking liquid.
In a wok or large pan over medium-high heat, pour in the vegetable oil and add the remaining 3 scallions, 3 ginger slices, the garlic, red chiles, remaining 3 star anise pods, the onion, rock sugar, and spicy bean paste. Cook until the onions start to become translucent.
Add the sliced beef.
Add the dark soy sauce, for color, stir, then add the rice wine.
Pour in the light soy sauce, for flavor, then add the tomatoes. Stir fry for 8-10 minutes.
Fill the same large pot about a quarter of the way with water and heat over medium-high heat. Add the stir-fried meat, vegetables, and cooking liquid.
Add more water until the meat is just covered, then add the white pepper, salt, and bay leaves. Cover and reduce the heat to low and simmer for at least 2 hours, until the meat becomes tender. Remove the bay leaves and star anise before serving.
Bring a large pot of water to boil over high heat and cook the flour noodles according to the package instructions. Remove the noodles from the water.
Add the bok choy to the boiling water. Cook for 3 minutes, then remove.
To assemble the soup, place a generous amount of noodles in the bottom of a bowl. Then, add bok choy, meat, and broth. Garnish with scallions, cilantro, and red chilies.
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