The transcriptome, proteome, and metabolome are the flexible material basis for the stable plant genotypes to produce the dynamic phenotypes that change with the environment. The fitting of the transcriptome, proteome, and metabolome into metabolic pathways in plants commonly requires complex and ectopic biotechnology experiments. Spatial multiomics technology led by mass spectrometry imaging (MSI) can provide the most intuitive in situ evidence chain through the spatial association of related transcription factors, functional proteins, and metabolites in the pathway. This spatial evidence can be associated with space, time, plant morphology, tissues and organs, and provides the most direct physiological evidence for the dynamic relationship between plant phenotypic changes and their macromolecular or small molecule components. The instrumental basis of how MSI can achieve high-throughput in situ spatial metabolic data acquisition and the factors affecting imaging quality are introduced. The last 3–4 years of this spatial evidence reflecting specific plant molecular physiology applications, including the spatial biosynthesis pathway of plant natural products, the material exchange between plant roots and the external environment, the physiological resistance of plants under abiotic stress, the chemical defense of plants under biological stress, and the interaction between plants and microorganisms are summarized. Finally, the possibility of spatial multiomics combined with phenotypic techniques to achieve spatiotemporal consistency in genotype-transcriptome-proteome-metabolome-phenotype in future plant physiology studies are discussed and the difficulty of mining plant physiological information from spatial data is examined.