The storage root of alligatorweed [Alternanthera philoxeroides (Mart.) Griseb.] growing in terrestrial habitats is an important metamorphic organ for its propagation, overwintering, and spread. However, the regulatory mechanism adventitious root expansion to form storage roots is still unclear. To reveal the changes accompanying the root-swelling process, we quantified sugar, soluble protein, and phytohormone content in adventitious and storage roots. Results demonstrated that sucrose, fructose, and soluble protein increased in storage roots, whereas abscisic acid (ABA), indoleacetic acid (IAA), brassinosteroid (BR), gibberellin, jasmonic acid, and cytokinin (trans-zeatin [tZ] and isopentenyladenine [iP] and the corresponding ribosides tZR and iPR). tZ-type (tZR and tZ) content decreased, suggesting the involvement of sugars and hormones in the formation of storage roots. To further reveal the molecular basis of A. philoxeroides’s ability to form storage roots and provide candidate genes for molecular function analyses, we assembled a de novo transcriptome of A. philoxeroides based on four sets of RNA-sequencing data. According to functional annotation and expression profiling, 42 unigenes involved in sucrose synthesis and hydrolysis were identified, in addition to 70, 58, and 78 unigenes in ABA, BR, and IAA signal transduction, respectively. The quantitative reverse transcriptase polymerase chain reaction analysis revealed 21 unigenes involved in sugar metabolism and hormone signal transduction were differentially expressed during the formation of storage roots. These results revealed metabolic changes during the formation of storage roots and provide candidate genes involved in sugar and phytohormone metabolism in A. philoxeroides.