The invention belongs to the field of agriculture, and discloses a silicon-calcium capsule fertilizer suitable for the modern agriculture and a preparation method thereof. The silicon-calcium capsule fertilizer comprises the following components: tailing slag, ammonium sulfate, agricultural magnesium sulfate, agricultural zinc sulfate, agricultural ferrous sulfate, agricultural borax, silicon dioxide, soluble starch, trace elements, bentonite, a hydrophilic polymer material, a surfactant, citric acid powder, amino acid, cortex meliae, fructus quisqualis, Chinese gall, pubescent holly root, soapberry episperm, rhizoma atractylodis, and cellulase. The silicon-calcium capsule fertilizer is practical and is capable of effectively solving the problems of insects, diseases, nutritional imbalance, low fertilizer utilization rate, and soil salinization.