This work demonstrates how to improve the size distribution of silicon nanocrystals (Si-NCs) synthesized in a remote plasma, in which the flow dynamics and the particular chemistry initially resulted in the formation of small (2–10 nm) and large (50–120 nm) Si-NCs. Plasma consists of two regions: an axially expanding central plasma beam and a background region around the expansion. Continuum fluid dynamics simulations demonstrate that a significant mass flow occurs from the central beam to the background region. This mass flow can be gradually reduced upon confinement of the central beam, preventing the mass transport to the background region. Transmission electron microscopy and Raman spectroscopy analyses demonstrate that the volume fraction of large Si-NCs decreases from ~77% to below 45% in parallel with the decrease of mass flow to the background region upon confinement, which indicates that large Si-NCs are synthesized in the background and small Si-NCs are synthesized in the central beam. Spatially resolved ion flux analyses demonstrate that the ions are localized in the central beam despite the mass flow to the background, indicating that the formation of small Si-NCs is governed by ion-assisted growth while the formation of large Si-NCs is governed by radical-neutral-assisted growth in the absence of ions. According to these observations, a better uniformity in the size distribution of Si-NCs can be obtained by creating a more uniform plasma flow and controlling the density of plasma species in the plasma.