The threshing cylinder will wear and deform during the threshing process, causing dynamic balance problems. The combine harvester has multiple vibration excitation sources and a complex vibration environment, making it challenging to extract weak unbalanced signals from strong background noise. A novel three-step filtering framework is proposed in this paper. A zero phase filter was used as the pre-processing layer to filter out the high frequency components in the original signal and reduce the number of parameter-adaptive variational mode decompositions (PAVMD) needed. The PAVMD was used to decompose the non-stationary vibration signal before Adaptive Neuron Linear (Adaline) function was used to fit sinusoidal signal parameters. A measurement index, termed the correlation amplitude (CA) index, is constructed. The parameterisation of PAVMD was guided by the CA index, and the modal component of the unbalanced fault features were located. The simulation and real cylinder signals proved that the proposed method could effectively extract unbalanced signals under noise interference, and the unbalance was identified accurately by the influence coefficient method. Experiments on a threshing cylinder showed that the amplitude identification error was <24 g in single-sided unbalance identification, and the amplitude identification error was <27 g in double-sided unbalance identification. The proposed method had high robustness and small identification error, especially under short-time working conditions, compared with other similar approaches.