Image segmentation technology can effectively extract the foreground target in the image. However, the microbial image is easily disturbed by noise, its greyscale has the characteristics of nonuniform distribution, and several microorganisms with diverse forms exist in the same image, resulting in insufficient accuracy of microbial image segmentation. Therefore, a multithreshold microbial image segmentation algorithm using improved deep reinforcement learning is proposed. The wavelet transform method is used to remove the noise of the microbial image, the threshold number of the microbial image after denoising is determined by calculating the number of peaks of the grey histogram, and the foreground target of the microbial image is enhanced by the mean iterative threshold segmentation method, the preliminary segmentation of the microbial image is realized, the multithreshold microbial image segmentation model based on ResNet-Unet is constructed, and the cavity convolution and dual Q network mechanism are introduced to improve the segmentation model. The preliminary segmented microbial image is input into the improved segmentation model to realize the segmentation of the multithreshold microbial image. The results show that the proposed algorithm can effectively remove the noise of microbial images. With the increase in the number of thresholds, the peak signal-to-noise ratio, structural similarity, and feature similarity show an upward trend, and the loss rate of the model is less than 0.05%. The minimum running time of the algorithm is 3.804 s. It can effectively and quickly segment multithreshold microbial images and has important application value in the field of microbial recognition.