Vibration is complicated in run-up and coast-down process of rotating and reciprocating combustion machinery which has multiple independent axles. Orders thatfrequency interact in different axle reference cause beating phenomena which makes order separation difficult. Through studying haracteristic of periodic loading machine system, vibration model including state equation and observation equation was constructed. Order tracking was implemented by decouple adaptive filter and crossing order was separated and extracted. Adaptive filter order tracking method overcomes shortcoming that fail to separate crossing order of other order tracking methods.