We have simulated a monolithic three-dimensional inverter (M3DINV) structure by considering the interfacial trap charges generated thermally during the monolithic three-dimensional integration process. We extracted the SPICE model parameters from M3DINV structures with two types of inter-layer dielectric thickness TILD (=10,100 nm) using the extracted interface trap charge distribution of the previous study. Logic circuits, such as inverters (INVs), ring oscillators (ROs), a 2 to 1 multiplexer (MUX), and D flip-flop and 6-transistor static random-access memory (6T SRAM) containing M3DINVs, were simulated using the extracted model parameters, and simulation results both with and without interface trap charges were compared. The extracted model parameters reflected current reduction, threshold voltage increase, and subthreshold swing (SS) degradation due to the interface trap charge. HSPICE simulation results of the fanout-3 (FO3) ring oscillator considering the interface trap charges showed a 20% reduction in frequency and a 30% increase in propagation delay compared to those without the interface trap charges. The propagation delays of the 2 × 1 MUX and D flip-flop with the interface trap charges were approximately 78.2 and 39.6% greater, respectively, than those without the interface trap charges. The retention static noise margin (SNM) of the SRAM increased by 16 mV (6.4%) and the read static noise margin (SNM) of SRAM decreased by 43 mV (35.8%) owing to the interface trap charge. The circuit simulation results revealed that the propagation delay increases owing to the interface trap charges. Therefore, it is necessary to fully consider the propagation delay of the logic circuit due to the generated interface trap charges when designing monolithic 3D integrated circuits.