The invention discloses a modified metakaolin-based permeation-resistant and crack-resistant agent for concrete. The modified metakaolin-based permeation-resistant and crack-resistant agent for concrete comprises: by mass, 10 to 75% of modified metakaolin, 5 to 40% of fine limestone powder, 4 to 40% of superfine coal ash, 1 to 20% of calcined hydrotalcite, 2 to 40% of fine quartz sand and 0.2 to 20% of solid silane powder. A preparation method of the modified metakaolin comprises the following steps of putting dry and washed kaolin into a bowl mill, carrying out grinding to obtain kaolin powder, carrying out calcination of the kaolin powder at a temperature of 500 to 1000 DEG C for 0.5 to 6.0 hours to obtain metakaolin, putting the metakaolin into a dispersion machine, adding an organic modifier of sulfamate or triethanolamine into the metakaolin, wherein a mass ratio of the metakaolin and the organic modifier is in a range of (5000: 1) to (100: 1), and carrying out dispersion to obtain the modified metakaolin having a contact angle of 50 to 100 degrees and a specific surface area of 8000 to 15000m<2>/kg. The modified metakaolin-based permeation-resistant and crack-resistant agentfor concrete can be utilized as a concrete additive, improves strength of concrete at different ages, does not produce obvious influences on concrete work performances, obviously improves anti-chloride ion penetration capability of concrete, reduces total shrinkage of concrete and improves crack resistance of concrete.