Frequency selective surface (FSS) is of great research interest for its wide applications in radome, absorber, electromagnetic filters, and artificial electromagnetic bandgap materials. In order to achieve a multifunctional FSS with real-time manipulated radar cross-section (RCS), there are mainly three ways, i.e. to design reconfigurable FSS unit cell, reconfigurable screen, and a combination of reconfigurable unit cell and screen. In this work, a combination design of both the reconfigurable unit cells and FSS screen is proposed to realize a dual-band FSS absorber with real-time manipulated RCS. For the reconfigurable unit cell, an angular ring and a meander cross dipole are combined to obtain a dual-band absorption. The dual-band resonance frequencies are reconfigurable by switching the PIN diodes embedded in the unit cell. When switching the PIN diodes, the resonance frequencies of the unit cell would be changed due to the variation of the effective capacitance and inductance of the unit cell. For the reconfigurable FSS screen, a novel biasing network is introduced, then the scattering field from each unit cell is modulated independently by switching the “on/off” state of the PIN diode through using a programmable field programmable gate array (FPGA). The total scattering far field is expressed as the superposition of the scattering field from each unit cell, and the far field scattered by the unit cell which is evaluated under an infinite periodic boundary condition. The scattering field of the FSS absorber can be predicted by considering the working states of all the unit cells on the screen. We define the unit cell as state “0”, when all the PIN diodes are at the states of “off”, and as state “1” when the PIN diodes are all at the states of “off”. The entire screen of FSS absorber is thus pixelated, which can be expressed by a binary coding matrix. The real-time scattering fields from the FSS absorber are manipulated perfectly by optimizing the states matrices showing “on/off” of each unit cell with genetic algorithm (GA). The FSS absorber is fabricated and measured. The ranges of 33dB and 25dB reconfigurable monostatic RCS at 3.2 GHz and 10.3 GHz are achieved by coding the states of unit cells on the FSS absorber screen. Both full-wave and analytical simulations demonstrate the effectiveness of the proposed optimization procedure. Compared with the reported FSS absorber, the proposed design is validated to possess good performance.