The complex engine operation environment will result in interference while utilizing ion current detection technique to achieve real timing monitoring of the combustion consequentially. Anti interference design of the detection system was optimized. An experiment was done on a spark ignition homogeneous charge compression ignition (SI HCCI) engine. Results show that high voltage isolation module can protect collection system well; using capacitance to isolate ignition can reduce the interference from background; capacitance detection method cannot reflect accurately when knock phenomenon happens. Eliminating zero drift with a software achieves good effect. With the optimized ion current detection system, the ratio of signal to noise of ion current increases significantly in HCCI combustion.