A new multiscale coarse-graining procedure is used to study carbonaceous nanoparticle agglomeration in combustion environments. The computational methodology is applied to an ensemble of 10,000 nanoparticles (or effectively 2 million total carbon atoms) to simulate, for the first time, the agglomeration of carbonaceous nanoparticles using coarse-grained atomistic-scale information. In particular, with the coarse-graining approach we are able to assess the influence of nanoparticle morphology and temperature on the agglomeration process. The coarse-graining of the interparticle force field is accomplished applying a force-matching procedure to data obtained from trajectories and forces from all-atom MD simulations. The coarse-grained MD results show rich and varied clustering behaviors for different particle morphology and, in some cases, the formation of primary particles with a diameter around 15 nm are observed for the first time by molecular simulation techniques.