The invention discloses a method for cipher card multi-algorithm parallel execution. The method is applied to a PCI-E cipher card which is constituted based on an FPGA. The method comprises the stepsof setting a preset number of Function in an IP core according to the number of algorithms of the PCI-E cipher card, and configuring the same algorithm living example and configuration information forthe Function, so that an identification terminal identifies a preset number of PCI-E cipher cards; naming all Function named after corresponding function numbers according to a preset rule, and calling the Function corresponding to all the function numbers according to an instruction of a client layer API. A logic calculation resource can be more scientifically and reasonably utilized, the hardware resource utilization rate is higher, multiple algorithms at the same time or at the same time interval are all in the operation state, and the operation efficiency is obviously improved. The invention further discloses a system for cipher card multi-algorithm parallel execution, the PCI-E cipher card, and a computer readable storage medium, and the system for cipher card multi-algorithm parallel execution, the PCI-E cipher card, and the computer readable storage medium have the advantages.