The invention, which relates to the technical field of food processing, provides flavored hot pickled mustard tubers and a preparation method thereof. The flavored hot pickled mustard tubers is prepared by using the following raw materials: green vegetable heads, a soaking solution, phytic acid, sodium erythorbate, disodium stannous citrate, citric acid, lactic acid bacteria, sodium alginate, protease and table salt. According to the invention, the flavored hot pickled mustard tubers having crisp and tasty taste, moderate acidity, and unique flavor has extremely low nitrite content and is a nutritional and safe preserved hot pickled mustard tuber product; the sensory quality is improved, the nutritional value is increased, the shelf life is prolonged, so that the healthy consumption concept of modern consumers is met; the lactic acid bacteria are used for pickling the mustard tuber, so that the cost is saved, the food safety of the hot pickled mustard tuber is improved, the flavor of the hot pickled mustard tuber is improved, the quality and functionality of the hot pickled mustard tuber are enhanced. The preparation method is a novel safe and reliable process; production of harmful microorganisms in the preparation process of the hot pickled mustard tuber is reduced, the flavor of the hot pickled mustard tuber is ensured and the shelf life is prolonged.