Biomass is a unique renewable carbon resource that can be flexibly converted into biofuels, chemicals, and biomaterials using pyrolysis technology. Microwave-assisted pyrolysis (MAP) has gained increasing attention due to its faster and more uniform heating characteristics compared to conventional pyrolysis (CP). However, thermodynamic assessments of biomass MAP-based systems that consider detailed pyrolytic product information are lacking. This study simulated biomass-derived poly-generation systems employing MAP with microwave absorbers (MAP-S) and CP with solid heat carriers (CP-S). The proposed systems included pretreatment, pyrolysis, bio-oil rectification, hydrodeoxygenation, and combined cycle power units, producing biofuels, chemicals, and electricity. To obtain operating information that aligns more closely with engineering reality, pilot-scale numerical models integrating reaction kinetics and transport processes were established for the MAP and CP reactors. These models were validated against lab-scale experimental results after scaling down the models’ geometrical sizes. The results of product yields and energy consumption from numerical simulations were used to support the process simulation. Simulation results showed that the energy efficiency and net power generation efficiency of MAP-S were 59.37 % and 17.78 %, respectively, lower than the 67.19 % and 18.22 % of CP-S. In CP-S, the exergy of materials primarily moved towards the chemicals production units with an exergy efficiency (ηex) of 60.0 %, whereas in MAP-S, more exergy flowed towards the power generation units with a lower ηex of 58.46 %. Notably, the exergy destruction rate (Exd) for CP-S was 3.91 MW, higher than the 3.65 MW for MAP-S. Moreover, the CP-S achieves a higher carbon utilization efficiency at 42.32 %, compared to 35.03 % for the MAP-S. For the pyrolysis units, although the CP unit experienced higher heat losses (0.31 MW) compared to the MAP unit (0.1 MW), the ηex for the CP unit was higher due to a lower Exd. Additionally, CP-S consumed more hydrogen in the hydrodeoxygenation units, whereas MAP-S might achieve self-supply of hydrogen by adjusting operation conditions and technology processes.