This paper describes knocking combustion in a diesel homogeneous charge compression ignition (HCCI) engine. The knocking combustion was investigated by a harmonic analysis, and the complex logarithmic spectrum (CLS), calculated by Fast Fourier Transformation (FFT) based on the acquired in-cylinder pressure, was defined to evaluate the knocking intensity. The consistencies among maximum in-cylinder pressure, maximum pressure rise rate and knocking parameters of harmonic analysis were proved. The effects of engine load, speed, internal and external exhaust gas recirculation (EGR) on the knocking combustion in this HCCI diesel engine were experimentally studied. The results showed that the CLS in the range of 180th- to 350th-order harmonics was more sensitive to the knocking intensity, and the CLS increased with the increase in knocking intensity. The increasing of load, speed and internal EGR would increase the occurrence probability and intensity of the knocking combustion, but the increasing of the external EGR would decrease the occurrence probability. (C) 2012 Elsevier Ltd. All rights reserved.