In the field of images and imaging, super-resolution (SR) reconstruction of images is a technique that converts one or more low-resolution (LR) images into a highresolution (HR) image. The classical two types of SR methods are mainly based on applying a single image or multiple images captured by a single camera. Microarray camera has the characteristics of small size, multi views, and the possibility of applying to portable devices. It has become a research hotspot in image processing. In this paper, we propose a SR reconstruction of images based on a microarray camera for sharpening and registration processing of array images. The array images are interpolated to obtain a HR image initially followed by a convolution neural network (CNN) procedure for enhancement. The convolution layers of our convolution neural network are 3 3× or 1 1× layers, of which the 1 1× layers are used to improve the network performance particularly. A bottleneck structure is applied to reduce the parameter numbers of the nonlinear mapping and to improve the nonlinear capability of the whole network. Finally, we use a 3 3× deconvolution layer to significantly reduce the number of parameters compared to the deconvolution layer of FSRCNN-s. The experiments show that the proposed method can not only ameliorate effectively the texture quality of the target image based on the array images information, but also further enhance the quality of the initial high resolution image by the improved CNN.