The invention discloses a berberine multiple-capsule-wall-thickness microcapsule preparation and a preparation method thereof. The preparation comprises a microcapsule with at least two different capsule-wall-thickness ranges, wherein the capsule-wall-thickness ranges have different peak values. The microcapsule comprises a capsule core and a capsule wall, wherein the effective component of capsule core is berberine. It is shown through pesticide bioassay test results that the microcapsule preparation has a prevention and treatment effect on pests and diseases of tomatoes and cucumbers, has initial activity almost same as that of an aqueous solution, is obviously increased in lasting period, and can effectively reduce the drug damage on crops.