General aviation (GA) aircraft generally driven by aviation piston engines (APE) are currently experiencing promising growth globally. To relieve the fossil fuel scarce, the application of alternative fuels was extensively encouraged for green GA development. This study aims to investigate the suitability of using aviation kerosene rocket propellant 3 (RP-3) and its pentanol blends (by 30% volume fraction) in an aviation compression ignition (CI) engine, by comparing their combustion performance and emission characteristics differences under various injection timings with baseline diesel. The major combustion parameters including the in-cylinder pressure, heat release rate, ignition delay, combustion duration, indicated thermal efficiency (ITE), and indicated specific fuel consumption (ISFC) were evaluated as the crank angle (CA) 50 swept from 9 to 15° crank angle after top dead center (ATDC). The ITE of RP-3/Pentanol blends presented to be higher than those of diesel by 4.2%−5.0%, and pure RP-3 by 2.6%−3.4%. The improved ITE of the blended fuel is due to the longest ignition delay and the shortest combustion duration under all the CA50. Moreover, the particulate matter (PM) emissions with the number concentration, geometric mean diameter (GMD), size-resolved distribution characteristics were quantitatively analyzed for all the test fuels. RP-3/Pentanol dramatically reduced the number-based PM, by over 50% and two magnitudes of order lower than those of RP-3 and diesel, respectively. Improved PM emissions from the alcohol blends intensively was caused by the better premixing and evaporating states with subsequent homogeneous combustion. Additionally, the PM emissions of the three fuels exhibited different sensitivities to the varied injection timings. With the retardance of injection timings, the PM declined apparently for diesel and RP-3 due to prolonged ignition delay and decreased in-cylinder temperature, but remained nearly unchanged for RP-3/Pentanol because of the growth of nucleation mode PM.