This paper investigates pilot injection strategies to improve the combustion controllability of a premixed n-butanol cylinder charge while achieving ultra-low NOx emissions comparable to homogenous charge compression ignition (HCCI). Detailed insights are given for the ignition processes controlled by fuel and reactivity stratification. The n-butanol port injection is applied to form a homogeneous cylinder charge, an early pilot direct injection of either n-butanol or diesel is generated to control the ignition and combustion. In dual-fuel reactivity stratification combustion (RSC) strategy with an early diesel pilot injection, the prompt control of combustion phasing relies on fuel energy ratio adjustment. Under heavy EGR, the RSC can lower the NOx emissions to the level of 10 ppm and retain the combustion completeness, however, at the cost of increased pressure rise rate. EGR plays a key role in suppressing the pressure rise rate for load extension of RSC combustion. In order to maintain a moderate pressure rise rate when the engine load increases, the combustion phasing must be retarded through heavy EGR together with increased PFI n-butanol energy ratio, which leads to an efficiency penalty. In the single-fuel strategy, the early pilot injection of n-butanol results in fuel stratification in the cylinder which is responsible for the combustion initiation. The single-fuel strategy retains effective ignition controllability although the start of combustion manifests less sensitivity to the n-butanol pilot injection timing. In the tested low to medium engine load range, the single-fuel strategy can achieve NOx emissions level same to HCCI combustion, while the NOx emissions of dual-fuel RSC strategy are slightly higher because of the reactivity gradient and more advanced combustion phasing.