The present invention discloses a multielement chelating silicon-rich rice seedling fertilizer and a manufacturing method thereof, the rice seedling fertilizer comprises ammonium nitrate phosphate, calcium superphosphate, potassium sulfate, magnesium sulfate heptahydrate, humic acid, rice husk powder, high temperature water quenched silicon calcium powder, concentrated sulfuric acid, zinc sulfate, ferrous sulfate, copper sulfate, borax, manganese chloride tetrahydrate, complex nutritional type chelating agent (potassium tripolyphosphate + ammonium citrate + fumaric acid) and brassinolide milk powder. The multielement chelating silicon-rich rice seedling fertilizer can be obtained by evenly mixing the biodegradable chelates formed by chelation reaction, the acidified high temperature water quenched silicon calcium powder, and other substances, by use of the multielement chelating silicon-rich rice seedling fertilizer, the fertilizer utilization rate is improved, disease resistance in rice seedlings can be enhanced, root system is well developed, seedlings are thick and strong, seedlings are quick to recover after transplanting, tillering is increased, and the multielement chelating silicon-rich rice seedling fertilizer is an environmentally friendly new rice seedling fertilizer.