In this work, an active injection control strategy is developed for enabling clean and efficient combustion on an ethanol-diesel dual-fuel engine. The essence of this active injection control is the minimization of the diffusion burning and resultant emissions associated with the diesel injection while maintaining controllability over the ignition and combustion processes. A stand-alone injection bench is employed to characterize the rate of injection for the diesel injection events, and a regression model is established to describe the injection timings and injector delays. A new combustion control parameter is proposed to characterize the extent of diffusion burning on a cycle-to-cycle basis by comparing the modelled rate of diesel injection with the rate of heat release in real time. The test results show that the proposed parameter, compared with the traditional ignition delay, better correlates to the enabling of low NOx and low smoke combustion. Particularly in the ethanol-diesel dual-fuel combustion, this new parameter can be controlled by actively adjusting the fuel ratio for each engine cycle. An active injection control strategy is therefore implemented to simultaneously control the engine load, combustion phasing, and the extent of diffusion burning via cycle-to-cycle adjustments on the fuelling rates, fuel ratio, and the diesel injection timing respectively. The control is validated by engine tests, and efficient combustion is achieved up to 19.5 bar IMEP with low NOx and low smoke emissions.