A three-dimensional simulation was carried out for investigating effects of negative valve overlap (NVO) on gas exchange and fuel-air mixing processes in a diesel homogeneous charge compression ignition (HCCI) engine with early fuel injection. It was found that the case with longer NVO produced a stronger swirl motion and a more significant vortex below the intake valve due to the high annular jet flow through the valve curtain area during the intake stroke. However, there was not much difference in the values of swirl ratio, tumble ratio and turbulence intensity between different NVOs at the end of compression stroke. It was also seen that enlarged NVO not just increased in-cylinder temperature but also improved the temperature homogeneity. With increased NVO, there is a bigger spray shape and more droplets exist in gaps of sprays. This demonstrates that stronger turbulence intensity and higher temperature homogeneity with higher NVO improve fuel vaporization and air-fuel mixing.