The invention provides a method and a system for producing Mo-99 by using a liquid molten salt reactor. The method comprises the following steps: providing a liquid molten salt reactor, wherein a plurality of graphite moderation assemblies containing channels are arranged in the reactor core, the channels of the graphite moderation assemblies are filled with molten salt composed of low-enriched uranium and base salt, and Mo-99 is generated by fission in the liquid molten salt reactor. When the liquid molten salt reactor runs, an on-line solid-liquid separation method is adopted to separate indissolvable solid fission products on line, then a cooling method is adopted to reduce the radioactive activity of the indissolvable solid fission products, and finally a chemical separation method is adopted to separate and recover Mo-99 from the indissolvable solid fission products, so that the preparation of Mo-99 is realized. According to the invention, the production efficiency is improved, operation is convenient and fast, the economic cost is low, the fuel demand quantity is low, the radioactive shielding requirement is low, and the current Mo-99 supply demand problem can be effectively solved.