This paper presents a computational investigation of the in-cylinder charge characteristics within a motored 4-valve direct injection HCCI engine cylinder with applied negative valve overlapping. Non-typical intake valve strategy was investigated; whereby the pair of intake valves was assumed to follow the same low-lift short-duration valve-lift profile but actuated at different timings. The phase of intake-valve-opening relative to that of exhaust-valve-closing was optimized in terms of pumping losses. The flow fields generated with such an intake valve strategy were compared to those produced in the same engine cylinder but with typical early and late intake-valve-timing. The computational results of such an approach showed modifications in the in-cylinder swirl and tumble motions during the intake and compression strokes. Moreover, the intake generated in-cylinder flow structure developed by the application of non-identical intake-valve-timing was shown to be preserved and continued in the cylinder volume till the second half of the compression stroke. When compared with the typical early intake-valve-timing, the case of non-identical intake-valve-timing showed a significant enhancement of induction-produced turbulence similar to what was obtained by typical late intake-valve-timing but earlier on the intake stroke. Applying such an intake valve strategy in actual 4-valve engines is expected to improve the in-cylinder mixture preparation process as well as the combustion aspects of the homogeneous charge compression ignition (HCCI) combustion system.