Conventional sodium silicate gels commonly undergo rapid and poorly controlled gelation upon direct acidification, resulting in narrow operational windows and limited deep-placement capability. To overcome these limitations, an integrated mechanism-to-application evaluation was conducted on a pH-triggered, slow-gelling silica system governed by the controlled hydrolysis of an organic ester. By systematically comparing HCl with conventional short-chain and sterically hindered ester-based latent acid generators, triethyl citrate (TEC) was identified as an effective kinetic regulator due to its steric-shielding effect. The optimized formulation—comprising 2.5 wt% sodium metasilicate, 5 wt% TEC, 0.1 wt% nano-SiO2, and 0.1 wt% borax—exhibited a controlled gelation time of approximately 5 h at 90 °C. Dynamic light scattering, gel-strength evaluation, and microscopic characterization revealed that the system underwent hierarchical particle aggregation, ultimately evolving into a dense three-dimensional gel network with a maximum Sydansk gel strength code of H. Core flooding experiments demonstrated that the system combined high injectivity prior to gelation with robust strong plugging performance following thermal aging. In single-core tests, plugging efficiencies reached approximately 98% for the high-permeability core and 95% for the low-permeability core. In parallel dual-core flooding, the overall plugging efficiency was approximately 98%, and the flow ratio between the high- and low-permeability cores shifted from 9:1 to 3:7, and further to 1:9 following reverse flooding. These results indicate effective plugging of the dominant high-permeability channel and sustained flow diversion into the previously bypassed low-permeability zones. NMR T2 spectra and CT scans further supported this selective placement behaviour: the gel preferentially occupied the larger pore spaces of the high-permeability core, whereas the low-permeability core exhibited only minimal gel invasion, with invasion confined to the proximal 10% of the core length. Overall, the TEC-triggered silica gel system achieves delayed gelation, deep plugging, and flow diversion, offering a promising chemical strategy for profile control in strongly heterogeneous reservoirs.