Infectious diseases, bacteria resistance and environmental issues are very serious problems emerged recently in aquaculture and negatively impact to public health. The reason is lack of effectiveness in using antibiotics against the mentioned matters resulting in high residue of antibiotics in exposed animal and human body. Drug delivery nanosystems have been proved as great potential approach to obtain high efficacy in treatment of many types of diseases thanks to excellent ability in delivery and distribution of drug to the targeted sites. In this work Fe3O4 based drug delivery nanosystem loading doxycycline was prepared by multi-step procedure. Morphology, size, molecular structure, zeta potential and efficiency of loading antibiotic were determined by field emission scanning electron microscopy (FESEM), transmission electron microscopy (TEM), x-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), dynamic light scattering (DLS) methods. The results showed that the system have spherical shape and mean size of 103 nm and zeta potential of −38.9 mV. Therefore, the system was a nanosystem and stable in aqueous dispersion and could load doxycycline antibiotic up to 85.3%. Drug delivery nano system loaded doxycycline showed the efficacy, and prevention of disease on white leg shrimp. This system has the potential to provide effective prevention and treatment of disease in aquaculture.