Ion current sensing, which usually employs a spark plug as its sensor to obtain feedback signal from different types of combustion in SI engines, may be applied to HCCI combustion sensing instead of a prohibitively expensive piezoelectric pressure transducer. However, studies showed that the ion current detected by a spark plug sensor is a localized signal within the vicinity of the sensor's electrode gap, being affected by conditions around it. To find out better and feasible ion probe positions, a 3D-CFD model with a detailed surrogate mechanism containing 1423 species and 6106 reactions was employed to study the effect of stratification on ion distribution in HCCI combustion.The simulation results indicate that the monitor probe 1, 8 and 9 are more stable and reliable than the others. IONmax and dIONmax are more accurate to estimate CA50 and dQmax respectively. Because combustion starts near the shallow part of the piston bowl, timing offsets occur between CA10 and ION10 for spark plug sensors located near the cylinder head. As stratification becomes severe, spots with high H3O+ mole fraction appear near the cylinder head at CA10, thus reducing the lag between ion and heat release parameter phases.