It is of great significance to construct specially designed gold nanocrystals (AuNCs) with precisely controllable size and morphology to achieve an excellent physicochemical performance. In this work, sea urchin-shaped AuNCs with tunable plasmonic property were successfully synthesized by the hybridized double-strand poly adenine (dsPolyA) DNA-directed self-assembly technique. Hybridized dsPolyA as the directing template had suitable rigidity and upright conformation, which benefited the controllable formation of these anisotropic multi-branched AuNCs with the assistance of surfactant. The effects of essential conditions influencing the synthesis and precise morphology control were investigated in detail. COMSOL simulation was used to evaluate their electromagnetic field distribution according to their morphologies, and the result suggested that sea urchin-shaped AuNCs had abundant ‘hot spots’ for surface-enhanced Raman scattering (SERS) detection due to their regular nanoprotuberance structure. Finally, sea urchin-shaped AuNCs with excellent SERS and catalytic performance were applied for the quantitative analysis of food colorant and catalytic degradation of potential pollutants. The SERS enhancement factor of sea urchin-shaped AuNCs was up to 5.27 × 106, and the catalytic degradation rate for 4-NP by these AuNCs was up to −0.13min−1.