This study numerically investigated knocking phenomenal of a RCCI (Reactivity Controlled Compression Ignition) engine fuelled with biodiesel and methanol. A reduced biodiesel/methanol chemical reaction mechanism coupled with 3D-CFD model was developed and applied to capture local pressure and species concentrations at 10 different regions in the computational domain. A Butterworth band-pass filter was used to process local pressure traces and the maximum peak-to-peak of the filtered data was used to quantify the knocking intensity. Species concentrations analysis was applied to identify the engine knocking occurrence. Finally, knocking mitigations strategies using cooled EGR were assessed. In addition, based on numerical analysis, the effect of SOI (Start of Injection) and premixed methanol mass fraction on engine knocking were evaluated. The results showed that the filtered pressure signals and intermediate chemical species are favored methods to identify and predict engine knocking. Moreover, cooled EGR is an effective way to attenuate engine knocking. Retarded SOI and lower premixed methanol mass fraction could also suppress the engine knocking. (C) 2015 Elsevier Ltd. All rights reserved.