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The synthesis of partially substituted silicon hydroxyapatite (Si-HAp) nanopowders was systematically investigated via the microwave-assisted hydrothermal process. The experiments were conducted at 150 °C for 1 h using TMAS (C4H13NO5Si2) as a Si4+ precursor. To improve the Si4+ uptake in the hexagonal structure, the Si precursor was supplied above the stoichiometric molar ratio (0.2 M). The concentration of the TMAS aqueous solutions used varied between 0.3 and 1.8 M, corresponding to saturation levels of 1.5–9.0-fold. Rietveld refinement analyses indicated that Si incorporation occurred in the HAp lattice by replacing phosphate groups (PO43−) with the silicate (SiO4−) group. FT-IR and XPS analyses also confirmed the gradual uptake of SiO4− units in the HAp, as the saturation of Si4+ reached 1.8 M. TEM observations confirmed that Si-HAp agglomerates had a high crystallinity and are constituted by tiny rod-shaped particles with single-crystal habit. Furthermore, a reduction in the particle growth process took place by increasing the Si4+ excess content up to 1.8 M, and the excess of Si4+ triggered the fine rod-shaped particles self-assembly to form agglomerates. The agglomerate size that occurred with intermediate (0.99 mol%) and large (12.16 mol%) Si contents varied between 233.1 and 315.1 nm, respectively. The excess of Si in the hydrothermal medium might trigger the formation of the Si-HAp agglomerates prepared under fast kinetic reaction conditions assisted by the microwave heating. Consequently, the use of microwave heating-assisted hydrothermal conditions has delivered high processing efficiency to crystallize Si-HAp with a broad content of Si4+.