Here we report a mechanism investigation on the ordered aggregation of particles at a diffusion limitation. A gel solution is employed to create a diffusion limitation for the synthesis of silver particles. Diamond-shaped silver particles are largely generated in an agar gel solution. The time dependent characterization of samples indicates that the diamond-shaped silver particles are built up by the aggregation of primary nanocrystals. A molecular simulation is conducted to reveal this aggregation process. Under diffusion limitation these tiny crystals tend to aggregate by sharing the high energy facets of (100), while the low energy facets of (111) is largely exposed, which results in an oriented aggregation, forming diamond-shaped particles. This formation mechanism is confirmed by following experiments via conducting the synthesis in different gel systems at different gel addition. The results of this paper indicate that the diffusion of building blocks plays an important role in the structure development of aggregates, which was underestimated previously.