Detailed characteristics of morphology, nanostructures, and sizes were analyzed for particulate matter (PM) emissions from low-temperature combustion (LTC) modes of a single-cylinder, light-duty diesel engine. The LTC engines have been widely studied in an effort to achieve high combustion efficiency and low exhaust emissions. Recent reports indicate that the number of nucleation mode particles increased in a broad engine operating range, which implies a negative impact on future PM emissions regulations in terms of the nanoparticle number. However, the size measurement of solid carbon particles by commercial instruments is indeed controversial due to the contribution of volatile organics to small nanoparticles. In this work, an LTC engine was operated with various biofuel blends, such as blends (B20) of soy bean oil (soy methyl ester, SME20) and palm oil (palm methyl ester, PME20), as well as an ultra-low-sulfur diesel fuel. Injection timing was varied at 22°, 26°, and 30° before top dead center for each fuel. A commercial scanning mobility particle sizer (SMPS) was used to measure the particle number size distributions. Also, a unique thermophoretic sampling system was used to collect particulates directly from the engine exhaust stream to enable in situ particle sampling. Then, the morphology and nanostructures of aggregate particles were analyzed by using a high-resolution transmission electron microscope (HRTEM) and a custom image/data acquisition system. The SMPS data showed that large populations of nucleation mode particles smaller than 10 nm were observed for all the fuels at various injection timings. Also, the maximum number of particles was obtained at approximately 75 nm in mobility diameter, regardless of fuel type and injection timing. In addition, the mean mobility diameters similarly reduced from ~80 nm to 60 nm with advancing injection timing. In comparison, the transmission electron microscope (TEM) result showed that nucleation mode particles smaller than 10 nm are rarely observed, and primary particle and aggregate sizes are much smaller than those reported for conventional diesel engines. Further, it appeared that aggregate particles tend to be larger, from ~47 nm to 62 nm, in projected area equivalent diameter with injection timing. Soot particles are expected to become larger during the soot formation process with advancing injection timing, resulting from longer residence time and higher combustion temperature. Accordingly, the contradictory result between SMPS and TEM is thought to be related to volatile organics found at the nucleation mode particles. The fractal dimension study indicated that LTC soot appeared to be fractal-like in geometry, like diesel soot, and it tends to become less compacted aggregates with injection timing. The HRTEM examination revealed that LTC soot particles are structurally less ordered, with short-ranged fringe layers and rough outer surfaces of particles, than those from a referenced conventional diesel engine.