Carbon-based magnetic molecular junctions are promising candidates for nanoscale spintronic applications because they are atomically thin and possess high stability and peculiar magnetism. Herein, based on first-principles and non-equilibrium Green's function, we designed a carbon-based molecular spintronic device composed of carbon atomic chains, zigzag-edged graphene nanoribbon (ZGNR), and a perylene molecule. Our results show that the device exhibits integrated spintronic and spin caloritronic functionalities, such as the bias-voltage driven spin filtering effect, negative differential resistance effect and giant magnetoresistance, temperature-gradient driven spin Seebeck effect, thermal spin filtering effect, high thermal magnetoresistance, and thermal colossal giant magnetoresistance. Furthermore, considering the phonon vibration effect, the spin and charge thermoelectric figure of merits (ZTsp and ZTch) can be enhanced and the peak of ZTsp is much larger than that of ZTch, indicating the excellent thermospin performance. The asymmetrical contact configuration between the carbon atomic chain and perylene/ZGNR inhibits the phonon thermal conductivity significantly, leading to the optimal ZTsp and ZTch of 2.4 and 0.5 at 300 K, respectively. These results suggest multifunctional spintronic and spin caloritronic applications for the perylene-based molecular device.