The invention provides fish sauce seasoning adopting whitebait as a main raw material and a preparation method thereof. The whitebait sauce is made of the following raw and auxiliary materials in parts by weight: 35 to 50 parts of whitebait, 45 to 60 parts of water, 3 to 10 parts of pepper powder, 2 to 5 parts of black sesames, 1 to 3 parts of small sesame oil, 5 to 10 parts of vegetable oil, 0.1 to 0.5 part of aginomoto, 3 to 5 parts of garlic, 0.3 to 0.8 part of sugar, 8 to 15 parts of edible salt, 0.5 to 2 parts of white pepper, 0.25 to 0.40 part of guar gum, 0.10 to 0.12 part of carboxymethylcellulose and 6 to 12 parts of a deodorization agent. The preparation method comprises the following steps of after selecting, washing and salting the raw materials, primarily soaking the raw material in the deodorization agent, seasoning and stewing, deodorizing the raw material, and finally canning and sterilizing the whitebait. The whitebait sauce has the advantages that the natural anchovies is adopted, and the whitebait sauce is red brown and bright in color; the whitebait sauce is reasonable in formula, the deodorization agent is stable in performance, safe and toxic-free, the deodorization effect is good, and the flavor is unique; the nutrients are abundant, and functions of tonifying the deficiency, invigorating stomach, moistening the lung and alleviating the water can be realized; meanwhile, the production process is simple and reasonable, and the cost is low.