Photothermal nanoplatforms with small size, low cost, multifunctionality, good biocompatibility and in particular biodegradability are greatly desired in the exploration of novel diagnostic and therapeutic methodologies. Despite Fe3O4 nanoparticles (NPs) have been approved as safe clinical agents, the low molar extinction coefficient and subsequent poor photothermal performance shed the doubt as effective photothermal materials. In this paper, we demonstrate the fabrication of polypyrrole (PPy)-enveloped Fe3O4 NP superstructures with a spherical morphology, which leads to a 300-fold increase in the molar extinction coefficient. The basic idea is the optimization of Fe3O4 electronic structures. By controlling the self-assembly of Fe3O4 NPs, the diameters of the superstructures are tuned from 32 to 64 nm. This significantly enhances the indirect transition and magnetic coupling of Fe ions, thus increasing the molar extinction coefficient of Fe3O4 NPs from 3.65 × 10(6) to 1.31 × 10(8) M(-1) cm(-1) at 808 nm. The envelopment of Fe3O4 superstructures with conductive PPy shell introduces additional electrons in the Fe3O4 oscillation system, and therewith further enhances the molar extinction coefficient to 1.12 × 10(9) M(-1) cm(-1). As a result, the photothermal performance is greatly improved. Primary cell experiments indicate that PPy-enveloped Fe3O4 NP superstructures are low toxic, and capable to kill Hela cells under near-infrared laser irradiation. Owing to the low cost, good biocompatibility and biodegradability, the PPy-enveloped Fe3O4 NP superstructures are promising photothermal platform for establishing novel diagnostic and therapeutic methods.