<p>Internet of Things (IoT) has become extensively utilized in multiple domains, so does unmanned aerial vehicle (UAV) network. For UAV network, it belongs to the flying IoT. However, the open-source protocol, software, and complex trust relationships rendered them vulnerable to security threats. Therefore, UAV system secure situation modelling and trust evaluation are pivotal. Petri net (PN) is such a powerful instrument for modelling complex systems. Compared with PN, fuzzy Petri net (FPN) can better characterize uncertainty and fuzziness knowledge in complex systems. However, the existing FPN models either use reachable tree for analysis and inference or use existing operators for computing equivalent inputs of transitions or fail to fully express fuzzy knowledge information. We propose interval-valued Pythagorean fuzzy Petri net (IVPFPN) to tackle these issues, and the developed IVPFPN also utilizes matrix operations for inference. Additionally, we develop a new operator for computing transitions’ equivalent inputs. Specifically, we propose interval-valued Pythagorean fuzzy matrix (IVPFM). Then, some operations and properties are probed. Further, we propose a novel aggregation operator, which satisfies idempotence, boundedness, and monotonicity. Some operations between matrices and the aggregation operator are used for parallel reasoning. Finally, simulation experiments elucidate that the proposed IVPFPN is effective as the inference efficiency of our model has improved by 16.2%.</p>