Abstract Mass spectrometry imaging (MSI) is a vital tool in botanical research. Image fusion is introduced for resolution enhancement of MSI data from animal samples, but its application to plant MSI data resulted in unsatisfactory visualizations due to the distinct morphological characteristics of plant tissues. Herein, this study presents loss controlled residual network (LCRN), a workflow dedicated to the super‐resolution fusion of plant MSI data. The pipeline used a residual connection‐based neural network implemented with a novel loss metric called edge perceptual loss. Edge perceptual loss is developed for evaluating complex morphological information that can not be properly reflected by common image metrics, and its implementation in loss propagation is vital to the quality of the fusion result. Compared to existing deep learning‐based methods, LCRN is able to generate a high‐quality super‐resolution fusion image of extra high magnification (up to 20‐fold) that combined chemical and morphological information obtained from MSI and microscopy, respectively.