Recent advancements in cancer treatment have improved patient prognoses, but chemotherapy-induced cardiotoxicity remains a prevalent concern. This study explores the potential of F-base-modified aptamers for targeted drug delivery, focusing on their impact on cardiotoxicity. From the phosphoramidite, F-base functionalized Sgc8-F23 was prepared in an automated and programmable way, which was further reacted with Paclitaxel (PTX) to give the F-base modified aptamer Sgc8-paclitaxel conjugates (Sgc8-F23-PTX) efficiently. The conjugate exhibits prolonged circulation time and enhanced efficacy as precision anticancer drug delivery system. Echocardiographic assessments reveal no exacerbation of cardiac dysfunction post-Acute Myocardial Infarction (AMI), and no pathological changes or increased apoptosis in non-infarcted cardiac regions. Autophagy pathway analysis shows no discernible differences in Sgc8-F23-PTX-treated cardiomyocytes compared to controls, contrasting with increased autophagy with Nanoparticle albumin-bound -Paclitaxel (Nab-PTX). Similarly, apoptosis analysis shows no significant distinctions. Moreover, Sgc8-F23-PTX exhibits no inhibitory effects on hERG, hNav1.5, or hCav1.2 channels. These findings suggest the safety and efficacy of F-base-modified Sgc8 aptamers for targeted drug delivery, holding potential clinical applications. Further research is warranted for clinical translation and exploration of other drug carriers.