The gas emissions and particulate matter of non-road diesel engine fueled with Fischer-Tropsch diesel fuel were investigated. The test was carried out on a four-stroke, water-cooled, single-cylinder engine under different the exhaust gas recirculation (EGR) rates such as 0%, 15%, and 30% at 2,700 rpm, 25%, 50%, and 75% load. The test results showed that when the EGR rate is less than 15%, nitrogen oxides (NOx) are reduced significantly, while hydrocarbon (HC) and carbon monoxide (CO) are increased less than 5%. However, when the EGR rate was 30%, HC and CO were maximally increased to 13.2% and 13.3%, respectively. Additionally, the Field Emission Scanning Electronic Microscope test and Energy Dispersive Spectrometer test were conducted. With increase of EGR rates, the micromorphology of particles was mainly showed as chain-like status and the growth of number concentration of particle was mainly contributed by the nuclear particle when the engine was at 25% load. In contrast, the micromorphology of particles was principally showed as clustered-like status, and the aggregated particles were dominating growth at 50% and 75% load. Moreover, as EGR rates increased, the degree of agglomeration and carbon content were gradually decreased at 25% load. The test also showed the opposite tendency at 50% and 75% load.