Identification of agrochemical degradation metabolites occurring in soil, water, and crops, and assessment of their toxicity, are of great importance in view of food safety. Single crystal X-ray (SCX) analysis, the most powerful tool to determine a three-dimensional molecular structure, has rarely been utilized for agrochemical metabolites because only a trace amount of them can be isolated from the environment and crops, which makes it very difficult to obtain a suitable single crystal for SCX analysis. The crystalline sponge (CS) method is a novel technique for SCX sample preparation developed by Prof. Fujita,1 which utilizes a crystal of a metal-organic framework (MOF) as a precrystallized molecular container that can incorporate a wide variety of small molecules within the pores and arrange the molecules in a regular pattern according to the periodicity of the host crystal. SCX analysis of the resultant inclusion crystal facilitates direct observation of the molecular structure of the target analyte. Here we report the initial examples of the structure identification of agrochemical metabolites from only a few micrograms of them. We demonstrate that the SCX analysis clearly distinguished the metabolites with very similar structures, which is extremely challenging for a conventional method using nuclear magnetic resonance (NMR) and mass spectrometric (MS) analysis.