A rigorous surface integral equation approach is proposed to study the spontaneous emission of a quantum emitter embedded in a multilayered plasmonic structure with the presence of arbitrarily shaped metallic nanoscatterers. With the aid of the Fermi's golden rule, the spontaneous emission of the emitter can be calculated from the local density of states, which can be further expressed by the imaginary part of the dyadic Green's function of the whole electromagnetic system. To obtain this Green's function numerically, a surface integral equation is established taking into account the scattering from the metallic nanoscatterers. Particularly, the modeling of the planar multilayered structure is simplified by applying the layered medium Green's function to reduce the computational domain and hence the memory requirement. Regarding the evaluation of Sommerfeld integrals in the layered medium Green's function, the discrete complex image method is adopted to accelerate the evaluation process. This work offers an accurate and efficient simulation tool for analyzing complex multilayered plasmonic system, which is commonly encountered in the design of optical elements and devices.