To solve the problem of the weak knock characteristic extraction for a port-injected two-stoke spark ignition (SI) unmanned aerial vehicle (UAV) engine burning aviation kerosene fuel, which is also known as the Rocket Propellant 3 (RP-3), the Intrinsic modal Functions Energy (IMFE) method is proposed according to the orthogonality of the intrinsic modal functions (IMFs). In this method, engine block vibration signals of the two-stroke SI UAV engine are decomposed into a finite number of intrinsic modal function (IMF) components. Then, the energy weight value of each IMF component is calculated, and the IMF component with the largest energy weight value is selected as the dominant characteristic component. The knock characteristic frequency of the two-stroke SI UAV engine is obtained by analyzing the frequency spectrum of the dominant characteristic component. A simulation experiment is designed and the feasibility of the algorithm is verified. The engine block vibration signals of the two-stroke SI UAV engine at 5100 rpm and 5200 rpm were extracted by this method. The results showed that the knock characteristic frequencies of engine block vibration signals at 5100 rpm and 5200 rpm were 3.320 kHz and 3.125 kHz, respectively. The Wavelet Packet Energy method was used to extract the characteristics of the same engine block vibration signal at 5200 rpm, and the same result as the IMFE method is obtained, which verifies the effectiveness of the IMFE method.