The work aims to design a flexible heat sealing system of bioassay card based on PLC for practical production and apply it to the automatic encapsulation of bioassay card filled with detection liquid and glass bead. SolidWorks was used to draw the mechanical structure diagram for the parts of the heat sealing system and the assembly of the heat sealing system was established. The assembly was subjected to interference analysis while parts with interference conflict were modified. The mechanical structure of the heat sealing system was designed when it was confirmed that there was no interference conflict. The order of actions of actuating mechanisms was determined according to technological requirements. The program flow chart was drawn and the program was written in the method of sequential control design. In actual production, it would take 4.9993 s for the heat sealing system to encapsulate a single bioassay card. The encapsulation speed met the design requirements. With the heat sealing system, the bioassay card can be quickly encapsulated. Moreover, the encapsulation tightness is good, and the sealing film edge is smooth, which can satisfy the production requirements.