We investigate the Capacitance-Voltage (CV) measurement to study the electrically active boron doping in Si nanocrystals (ncSi) embedded in SiO2. The ncSi thin films with high resistivity (200–400 Ω cm) can be measured by using an inverted metal oxide semiconductor (MOS) structure (Al/ncSi (B)/SiO2/Si). This device structure eliminates the complications from the effects of lateral current flow and the high sheet resistance in standard lateral MOS structures. The characteristic MOS CV curves observed are consistent with the effective p-type doping. The CV modeling method is presented and used to evaluate the electrically active doping concentration. We find that the highly boron doped ncSi films have electrically active doping of 1018–1019 cm−3 despite their high resistivity. The saturation of doping at about 1.4 × 1019 cm−3 and the low doping efficiency less than 5% are observed and discussed. The calculated effective mobility is in the order of 10−3 cm2/V s, indicating strong impurity/defect scattering effect that hinders carriers transport.