Chitosan oligosaccharides have been reported to inhibit various tumors. However, the water-soluble marine plant oligosaccharide alginate oligosaccharide (AOS) has only rarely been reported to have anti-cancer effects. Moreover, the inhibitory effect of AOS on prostate cancer and the underlying molecular mechanism remain unknown. This study shows that AOS inhibited cell growth, which was consistent with the attenuation of α2,6-sialylation modification. Furthermore, AOS inhibited ST6Gal-1 promoter activity and thus affected transcriptional processes. In addition, AOS could activate the Hippo/YAP pathway and block the recruitment of both the coactivator YAP and c-Jun. Furthermore, YAP interacted with the transcription factor c-Jun and regulated the transcriptional activity of the downstream target ST6Gal-1 gene. Consistent with in vitro data, AOS suppressed the tumorigenicity of prostate cancer cells via the Hippo/YAP pathway in vivo. In summary, these data indicate that AOS slows the proliferation of prostate cancer and provides a basis for the healthy function of kelp in traditional cognition.