Despite thousands of sex-biased genes being found in chickens, the genetic control of sexually dimorphic and left-right asymmetry during gonadal differentiation is not yet completely understood. This study aimed to identify microRNAs ( miRNAs ), long noncoding RNAs ( lncRNAs ), messenger RNAs ( mRNAs ), and signaling pathways during gonadal differentiation in chick embryos (day 6/stage 29). The left and right gonads were collected for RNA sequencing. Sex-biased, side-biased miRNAs, lncRNAs, mRNAs, and shared differentially expressed miRNAs ( DEmiRNA )–differentially expressed mRNAs ( DEmRNA )–differentially expressed lncRNAs ( DElncRNA ) interaction networks were performed. A total of 8 DEmiRNAs, 183 DElncRNAs, and 123 DEmRNAs were identified for the sex-biased genes, and 7 DEmiRNAs, 189 DElncRNAs, and 183 DEmRNAs for the side-biased genes. The results of quantitative real-time PCR were generally consistent with the RNA-sequencing results. The study suggested that miRNAs and lncRNAs regulation were novel gene-specific dosage compensation mechanism and they could contribute to left-right asymmetry of chicken, but sex-biased and side-biased miRNAs, lncRNAs, and mRNAs were independent of each other. The competing endogenous RNA ( ceRNA ) networks showed that 17 target pairs including miR-7b ( CYP19A1 , FSHR , GREB1 , STK31 , CORIN , and TDRD9 ), miR-211 ( FSHR , GREB1 , STK31 , CORIN , and TDRD9 ), miR-204 ( FSHR , GREB1 , CORIN , and TDRD9 ), and miR-302b-5p ( CYP19A1 and TDRD9 ) may play crucial roles in ovarian development. These analyses provide new clues to uncover molecular mechanisms and signaling networks of ovarian development.