The invention relates to a micro droplet-type PCR instrument auto focusing method based on a neural network. The method comprises a first step of focusing module design in which a lighting light source is arranged at one end, the emitted light passes through a biochip and then passes through an objective lens and then enters a camera, the objective lens plays a role of focusing, and the position of the objective lens is controlled by an auto three-dimensional platform, a second step of focusing strategy formulation in which the position of the focus is measured in advance, training is carried out through a BP neural network, stable mapping is acquired, and during a later focusing process, several positions are measured, the belonging function type is determined, and the position of the focus measured in advance is acquired, a third step of focusing function selection in which contour waves in hyper wavelets are used as an image focusing evaluation processing function, and the measurement value is used as input of the neural network and a fourth step of image detection area selection. The position of the focus can be given quickly and accurately, and the accuracy and the focusing speed of the PCR instrument detection system are improved.