Salt-tolerant Helianthus tuberosus is a new economic crop and special habitats may have an effect on this plant’s metabolites, specifically secondary metabolites, such that novel or bioactive compounds are produced. The secondary metabolites of endophytic fungi derived from salt-tolerant Helianthus tuberosus as well as the relationship between the host and the fungi are worth investigating. Our group isolated 10 endophytic fungi from salt-tolerant Helianthus tuberosus tubers. Brine shrimp lethality experiment showed that one strain, Mucor sp. ht-7 has remarkable bioactivity. Seven compounds were obtained after scaled fermentation, extraction, and separation. The structures of these compounds were established using modern spectroscopic techniques. In addition, the bioactivity and relationship of secondary metabolites between endophytic fungus and host are discussed.