In conclusion, the clinical analysis revealed that decreased motilin was an independent risk factor in spleen deficiency-FD; furthermore, the serum metabonomics analysis yielded novel insights into small-molecule metabolic alterations in its progression, with 15 metabolites biomarkers continuously varying across the progression of FD, which could be applied as an additional diagnostic tool for detecting delayed gastric emptying of FD in practical clinic cases. Here, MLN is linked to Fabry disease.