Belonging to the technical field of concrete admixtures, the invention discloses a mineral based concrete densifying agent and its preparation method. The mineral based concrete densifying agent comprises the following components by weight: 65-75% of a mineral active component, 3-5% of a surfactant material, 20-30% of a nano-crystal seed, and 1-2% of a dispersion stabilizer. The preparation method includes: homogenizing the surfactant material, the nano-crystal seed, and the dispersion stabilizer in advance for 20-30min, then adding the above mass percent of mineral active component into the premixed material, and performing homogenizing for 20-30min, thus obtaining the mineral based concrete densifying agent. The mineral based concrete densifying agent provided in the invention takes a mineral base as the main component, is free of chlor-alkali and has no toxicity, thus having no adverse influence on the environment. Being able to significantly improve the anti-permeability, frost resistance, chemical erosion resistance and abrasion resistance and other durability performance of concrete, the mineral based concrete densifying agent is suitable for hydraulic concrete structural parts with durability requirements.