The invention provides a silicon dioxide aerogel mortar and a preparation method thereof, belongs to the technical field of mortar preparation, and mainly relates to mortar and a preparation method thereof, which aim at solving the problem of failure to meet current actual requirements of mortar property in the prior art. The silicon dioxide aerogel mortar is prepared from the following components in parts by weight: 100 parts of cement, 300 parts of sand, 0.08 to 0.5 part of defoaming agent, 10 to 20 parts of silicon dioxide aerogel microsphere, 25 to 40 parts of ethyl acrylate emulsion, 0.02 to 0.1 part of polymer powder, and 5 to 7 parts of water. The silicon dioxide aerogel mortar has the advantages that the sticking property of whole cement mortar is improved, the tension strength, rapture strength and sticking durability are greatly improved, the dry shrinkage is decreased, the cracking is reduced, and the anti-freezing property and anti-seepage property are improved.