The invention discloses a nanocellulose-pectin microcapsule and a preparation method and application thereof. The preparation method includes the following steps that (1) orange nanocellulose is subjected to oxidization with an oxidant, and then is subjected to cationic modified reaction with a modifier to obtain cationic nanocellulose; (2) a dextran solution containing pectin is prepared and recorded as a solution A; and a polyethylene glycol solution containing the cationic nanocellulose is prepared and recorded as a solution B; and (3) following steps (1) or (2) is adopted to prepare and obtain the nanocellulose-pectin microcapsule; (1) a millimeter level microcapsule is prepared through a drop injection method, drops of the solution A are dropped into the solution B, and a millimeter level nanocellulose-pectin microcapsule is obtained after reaction; and (2) a micron level microcapsule is prepared through a microcapsule granulator, the solution A is dropped and sprayed into the solution B, and then reacted in the microcapsule granulator to obtain a micron level nanocellulose-pectin microcapsule. The nanocellulose-pectin microcapsule has good biocompatibility and high biosafety.