Branched micro/nano Se was prepared by the redaction of L-Cys•HCl and H2SeO3 in hydrothermal method, as β-CD was used as soft template. The structures of products were characterized by SEM, TEM and XRD. Some important factors influencing the morphology of products were studied and discussed, including the amounts of soft template, the reaction temperature and the reaction time. The results showed that external causes had a potent effect on the morphology of micro/nano Se. The uniform branched micro/nano Se prepared under the optimal reaction condition was rhombohedral trigonal selenium t-Se0, but its crystallinity degree was low.