Abstract: The present disclosure relates to a single cell analysis system. Disclosed herein is an instrument for single cell processing. The instrument comprises: a motor component; a processing component, which comprises a processing chamber inside and multiple first connecting holes; a container, which comprises a sample collecting reservoir, a waste collecting reservoir, multiple sample loading reservoirs, multiple first microchannels, and a second microchannel; a chip, which is connected under the container and forms a gap with the container, the chip comprises a third microchannel, the bottom of the third microchannel comprises a microwell array; a snap component comprises a feeding beam and a snap body, and a first end of the feeding beam connects to the snap body and a second end of the feeding beam connects to the motor component; and a pneumatic component which connects with the multiple first connecting holes.