The invention relates to a production method of a bio-transformed selenium preparation and a production method of a selenium-enriched agricultural product. The production method of the bio-transformed selenium preparation comprises the following steps: preparing a culture medium in accordance with strain medium components, keeping the culture medium in a transparent glass bottle, sterilizing by virtue of a medical high-pressure sterilizing pot at 121 DEG C and keeping for 20min, taking out the culture medium, and inoculating a strain which is 10-20% of the amount of the culture medium when the culture medium is cooled to room temperature, wherein the inoculating process needs to be operated on a super-clean bench in a sterile environment, the temperature of a cultivating process is 25-35 DEG C, illumination intensity is 1500-3500Lux, the strain is cultivated for 3-6 days, and a grown culture solution is in dark red or brown and contains 0.2-0.8 to the power of 8 billion/mL living effective bacteria. The method disclosed by the invention has the beneficial effects that 1. inorganic selenium, which is low in bioactivity, is converted into organic selenium, which is high in bioactivity, through microorganism transformation, and the organic selenium is low in toxicity, safe to use and high in absorption and utilization rates in animals and plants; 2. the bio-transformed selenium preparation is broad in application scope and strong in applicability, and the preparation is free from regional limitation when used; and 3. the bio-transformed selenium preparation is convenient to use and simple to operate.