The present invention discloses a biological sample processing apparatus, the biological sample processing apparatus comprises a pipe column, a cover body and a holder; the pipe column has a first tubular body portion and a second tubular body portion, the pipe column is hollow and open at both ends, so that a flow passage is formed in the pipe column, one open end edge of the first tubular body portion is provided with a first opening, one open end edge of the second tubular body portion is provided with a second opening, and the average inner diameter of the first tubular body portion is greater than the average inner diameter of the second tubular body portion; the cover body is coaxially arranged on the first opening for connecting the first tubular body portion; the holder is coaxially arranged in the flow passage, and is used for holding a biological sample; the holder is provided with a plurality of through holes for passing of a reagent, and the reagent can reciprocatingly circulate in the flow passage. The biological sample processing apparatus is suitable for automated nucleic acid extraction to improve the overall efficiency and quality.