The misfire of one or more diesel cylinder and the abnormal clearance in the intake valve train of cylinder are common faults which affect the safety and the performance of the engine seriously. A new fault diagnosis method based on EEMD and instantaneous energy density spectrum is proposed here. The IMFs generated by EEMD can alleviate the problem of mode mixing and approach the reality IMFs. The instantaneous energy density of these IMFs can distinguish the faulty impacts clearly. The effectiveness of this method was demonstrated by analysis the vibration signals of misfire fault and abnormal clearance in the intake valve train of 3110 diesel.