The invention discloses a rod-shaped microcapsule using a lactic acid-based polymer microparticle as a template and a preparation method thereof. The preparation method comprises (1) mixing a positively charged polymer solution and rod-shaped template lactic acid-based polymer particles to obtain a mixed liquid 1, carrying out centrifugation, removing the supernatant, and carrying out washing and centrifugation to obtain first microparticles, mixing the first microparticles and a negatively charged polymer solution to obtain a second solution 2, and carrying out centrifugation and washing to obtain second microparticles, (2) repeating the step (1), and (3) adding a glutaraldehyde aqueous solution into the microparticles obtained by the step (2), carrying out crosslinking, and carrying out centrifugation and washing to obtain final microparticles, dissolving the lactic acid-based polymer in the final microparticles, and carrying out washing to obtain shell-controllable rod-shaped microcapsules using lactic acid-based polymer microparticles as templates. The rod-shaped microcapsule can carry functional components such as biomacromolecule drugs. The method of the invention has the advantages of easy control of a shape and simple operation. The rod-shaped microcapsule has good biocompatibility, biodegradability and no immunogenicity.