Background: PARP inhibitors exhibit significant lethality in tumors with BRCA1/2 mutations or homologous recombination defects; however, their clinical application is limited by the rarity of BRCA1/2 mutations, complex resistance mechanisms, and limited efficacy of monotherapy. Objective: This study aimed to investigate how Niraparib induces dysregulation of sphingolipid metabolism—particularly upregulation of the key enzyme SPHK1—in triple-negative breast cancer (TNBC) cells, and to elucidate a novel super-enhancer (SE)-mediated mechanism of Niraparib resistance. We also applied AI-based virtual screening to identify compounds targeting key nodes and develop strategies for sensitizing TNBC to Niraparib. Results: Niraparib induced sphingolipid metabolic imbalance and significantly upregulated SPHK1 in TNBC. Multi-omics analyses revealed that SPHK1 is regulated by a super-enhancer. Mechanistically, Niraparib inhibited PARylation of the transcription factor SP1, enhancing its occupancy at the SE region and reactivating its transcriptional activity, thereby promoting SPHK1 expression. This process activated pro-survival signaling pathways and conferred niraparib resistance. AI-facilitated virtual screening identified the natural compound Echinatin as a potent SP1 inhibitor, which stably binds to SP1 and exhibits marked synergistic effects with Niraparib. While targeting downstream SPHK1 also provided therapeutic benefit by enhancing the anti-tumor efficacy of Niraparib, Echinatin demonstrates a superior advantage due to its more favorable toxicity profile. Conclusions: Niraparib induces resistance through the SP1-SE-SPHK1 axis, whereas Echinatin effectively reverses this mechanism by inhibiting the upstream regulator SP1, significantly potentiating the efficacy of Niraparib. This study reveals a novel molecular mechanism underlying Niraparib resistance and proposes a promising combination therapy strategy.