Yes, but you may have to provide your self-defined metabolite set libraries. In addition, some metabolite set libraries are species independent - such as those based on chemical structures.
The metabolite set libraries are species specific. For example, the pathway library is only valid for mammalian species. While the metabolite sets based on diseases are only applicable for human.
However, MSEA allows users to upload their own metabolite set libraries for enrichment analysis. Therefore, if you want to perform enrichment analysis on data from species other than human being, you need to provide two files, one contains metabolite concentration data, the other contains the metabolite set library.