The invention discloses a convolution neural network structure searching method and a system based on an evolutionary algorithm. The method comprises the steps of inputting a data set and setting preset parameters to obtain an initial population. By the controller TC as the main thread popping the initial population into the queue q and opening the queue manager tq and the message manager tm, After the queue manager TQ is turned on, the untrained chromosomes in the queue Q are pop-up and decoded, and a worker manager TW as an independent temporary thread is started to calculate the fitness forthe training, Through the cooperation of controller TC, queue manager TQ, worker manager TW and message manager TM, the parallel search of convolution neural network structure based on evolutionary algorithm is completed and the best model is output. The invention can realize automatic modeling, parameter adjustment and training for a given data set, has the advantages of high performance, large-scale, flow-chart and good certainty, and is particularly suitable for deployment and implementation on a high-performance computer cluster.