This study investigates the in silico anti-arboviral potential of zoochemicals derived from the methanolic extract of Charybdis natator shell, alongside their larvicidal efficacy against Aedes aegypti 4th instar larvae. Through GC-MS analysis, 27 zoochemicals were identified, demonstrating promising in silico activity against molecular antiviral targets: DENV2 protease (PDB: 6MO1) for anti-dengue, RNA polymerase (PDB: 5U04) for anti-Zika, and nsP2 protease (PDB: 3TRK) for anti-chikungunya. A strong positive correlation (r = 0.726-0.889) in binding affinities (kcal/mol) suggests a consistent inhibitory mechanism across these targets. Furthermore, PASS analysis indicates higher probabilities of activity (Pa) for insecticidal properties compared to antiviral efficacy, highlighting their dual potential as larvicidal agents and antiviral candidates. The methanolic extract of Charybdis natator shell exhibited potent larvicidal activity against Aedes aegypti (LC₅₀ = 81.001 µg/mL) in a dose-dependent manner (R = 0.968). In silico analysis further elucidated its inhibitory action on key growth regulators of A. aegypti, underscoring its potential to disrupt larval development. These findings highlight the dual utility of C. natator shell extract in vector management and in mitigating the transmission of arboviral diseases such as Dengue, Zika, and Chikungunya. The extract's promise as an eco-friendly, cost-effective source for developing novel insecticidal and antiviral agents merits further exploration.