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Lung cancer is considered as one of the most serious disease worldwide. The progress of drug carriers based on nonmaterial, which selectively hold chemotherapeutic agents to cancer cells, has become a major focus in biomedical research. This study aimed to evaluate the growth inhibition and apoptosis induction of the human lung cancer cells (A-549) by Q-loaded SBA-15 conjugate system. Mesoporous silica nanoparticles (SBA-15) as host materials for transporting therapeutics medicaments were fabricated for targeted drug delivery toward lung cancer. With the objective of increasing bioavailability and aqueous solubility of flavonoids, SBA-15 was successfully loaded with the quercetin (Q)—a major flavonoid and characterized with the help of Fourier-transform infrared spectroscopy (FTIR) and transmission electron microscopy (TEM). The biological investigation on A549 cell line confirmed that the efficacy of Q-SBA-15 is much higher than only Q. Moreover, the apoptotic pathway of synthesized Q-SBA-15 NPs examined that the Q-SBA-15–mediated apoptosis via PI3K/AKT/mTOR signaling pathway. Thus, the newly conjugated Q-SBA-15 system improved the apoptotic fate through caspase-mediated apoptosis via PI3K/AKT/mTOR signaling pathway and hence, it can be potentially employed as an anticancer agent for lung cancer.