The absorption cross section (ACS) of silicon nanocrystals (Si NCs) in single-layer and multilayer structures with variable thickness of oxide barriers is determined via a photoluminescence (PL) modulation technique that is based on the analysis of excitation intensity-dependent PL kinetics under modulated pumping. We clearly demonstrate that roughly doubling the barrier thickness (from ca. 1 to 2.2 nm) induces a decrease of the ACS by a factor of 1.5. An optimum separation barrier thickness of ca. 1.6 nm is calculated to maximize the PL intensity yield. This large variation of ACS values with barrier thickness is attributed to a modulation of either defect population states or of the efficiency of energy transfer between confined NC layers. An exponential decrease of the ACS with decreasing temperature down to 120 K can be explained by smaller occupation number of phonons and expansion of the band gap of Si NCs at low temperatures. This study clearly shows that the ACS of Si NCs cannot be considered as independent on experimental conditions and sample parameters.