The invention discloses a biodegradable nanoparticle-entrapped oral colon-targeted micro-capsule and a preparation method thereof. The preparation method comprises the following steps: 1, dissolving drugs and degradable polymers in an organic phase and taking a solution containing polyvinyl alcohol or sodium cholate as a water phase for preparing drug nanoparticles; 2, dissolving an enteric-coated material in absolute ethanol; 3, dispersing the drug nanoparticles in absolute ethanol in which the enteric-coated material is dissolved; 4, preparing edible oil; 5, dropwise adding ethanol liquid into the edible oil, stirring, solidifying, and volatilizing to remove absolute ethanol; 6, centrifuging suspension liquid, collecting the micro-capsule in a lower layer, and washing by normal hexane. The prepared oral colon-targeted micro-capsule has a remarkable pH response, drugs in the micro-capsule are hardly released under the acidic conditions, a capsule material is dissolved under the pH value of enteric canal, the drug nanoparticles are released, the nanoparticles can be transferred to a target point, and the drugs are slowly released, so that the absorption rate of oral administration is greatly increased, the bioavailability is improved, and the treatment effect is enhanced.