Schistosomiasis is caused by Schistosoma infection and affects more than 200 million people worldwide. A large number of eggs produced by adult Schistosoma play central the role in host pathology and subsequent disease dissemination. However, the underlying mechanisms of egg production in Schistosoma still need to be further elucidated. Previously, we found that miR-31 was highly enriched in the female reproductive organs of Schistosoma japonicum (S. japonicum), which was shown to be associated with ovarian development. In the present study, we analyzed the potential targets of miR-31 including mRNA and long noncoding RNAs (lncRNAs) in S. japonicum by RNA seq combined with bioinformatics. Then, six putative targets of miR-31 including three mRNAs such as EWB00_000918, EWB00_004242, and EWB00_009323 and three lncRNAs such as LncSJG_010465, LncSJG_015374 and LncSJG_013128 were further analyzed their expressions in the parasites treated with miR-31 inhibitor by qPCR to confirm their potential regulations. Whole mount in suit hybridization (WISH) analysis of some miR-31 targets were carried out to determine their colocalizations with miR-31. Furthermore, we selected EWB00_009323, which is an eggshell synthetic protein and also a target of miR-31, to inhibit its functions by small interfering RNA. The results indicated that inhibition of EB00_009323 led to decreased oviposition and defective ovarian morphology. Overall, the potential targets of miR-31 including mRNA and lncRNAs were identified in female S. japonicum and the results indicated that miR-31 coordinates with its targets, at least EWB00_009323, play an important role in ovarian development and egg production.