Liquid helium (LHe) vitrification improves the post-thaw developmental competence of bovine germinal vesicle (GV) stage oocytes; however, the underlying key transcriptomic regulatory networks still unexplored. This study aimed to evaluate the mRNA and lncRNA transcriptomic and developmental competence of bovine GV stage oocytes vitrified with LHe versus liquid nitrogen (LN). Bovine GV-stage oocytes were vitrified using LHe or LN as the cryogen. Post-thaw developmental competence was assessed following in vitro maturation, in vitro fertilization, and in vitro culture. High-throughput sequencing was performed to profile mRNA and lncRNA expressions between the oocytes vitrified in LHe and LN, followed by functional enrichment and co-expression network analyses. The transcriptomic alterations were independently validated by RT-qPCR. The present study found that LHe vitrification significantly improved cleavage rate (43.0% vs. 33.6%) and blastocyst rate (12.1% vs. 8.5%) compared to LN (p < 0.05). Transcriptomic analysis identified 361 differentially expressed mRNAs and 137 differentially expressed lncRNAs between the two groups. GO and KEGG analyses revealed that these mRNAs were enriched in immune response and metabolic pathways, while the lncRNA target genes were associated with the mitotic DNA integrity checkpoint and homologous chromosome segregation. In silico co-expression network analysis predicted HORMAD1, CDYL, and TRIOBP as potential central hub genes. In conclusion, LHe vitrification enhances the developmental competence of bovine GV-stage oocytes, which may associate with distinct mRNA-lncRNA co-expression networks and specific molecular signatures related to meiotic integrity and stress adaptation. These findings provide valuable transcriptomic resources and potential biomarkers for optimizing oocyte cryopreservation.