An in-situ synthesized catalyst by polyoxometallate and silicon-containing molecular sieve comprises components as follows: the polyoxometallate, a VIII metal oxide and the silicon-containing molecular sieve. The components in part by weight are as follows: 0-30 parts of the polyoxometallate, 0-5 parts of the VIII metal oxide and 100-65 parts of the silicon-containing molecular sieve. The preparation method of the catalyst comprises the steps that organic amine is taken as a template agent, the silicon-containing molecular sieve is prepared by a silicon source and/or an aluminum source, the polyoxometallate is introduced during the preparation process, and crystallization, drying and calcination are conducted after full mixing, so that the catalyst is obtained. The catalyst is high in catalytic activity and good in stability, improves the hydrogen desulfurization reaction performance, and is an ideal hydrogen desulfurization and aromatization catalyst. The preparation method is simple, the operation is easy, and the preparation cost is low.