The invention discloses a biological sample processing system which comprises a system base plate, a glass slide placing platform, a sample cell, a biological sample dropping device, a sample processing cavity body, a control system and a human-computer interface, wherein the biological sample dropping device comprises a space motion mechanism, a pipetting device and a glass slide taking and putting device, and the space motion mechanism is controlled by the control system, so that a preset moving track is output by a moving part of the space motion mechanism, a glass slide is automatically arranged at the beginning of an experiment, a biological sample is automatically sucked and transferred onto the surface of the glass slide by the pipetting device, the glass slide is automatically removed after the completion of the experiment, and the temperature of the biological sample cell can be adjusted. According to the biological sample processing system disclosed by the invention, the automatic dropping operation of chromosomes can be performed in a high-throughput mode; the biological sample processing system has the advantages of small size, low production cost, convenience in installation and maintenance and low energy consumption and is especially suitable for analyzing cytogenetics; the dropping process automation of the chromosomes is realized, the analysis efficiency is improved, and the biological sample processing quality is guaranteed.