To address the problem of microfracture development, limited sweep efficiency of water flooding, and the tendency to form dominant flow channels after long-term water injection in the fractured low-permeability reservoir of the Chang 6 formation in Block W of Wuqi Oilfield—which makes it difficult for conventional plugging agents to achieve effective deep profile control—a pre-assembled core–shell phase-change profile control agent (TSAD) was developed. Dynamic light scattering particle size analyzer, rotational viscometer, microfracture piston extrusion device, and core flooding experimental setup were used to systematically study the particle size distribution, phase-change characteristics, plugging strength, and water-plugging/oil-displacement performance of the TSAD agent. The results showed that the TSAD droplets had a particle size distribution of 20–300 nm, exhibiting good injectivity. The phase-change time could be controlled within 5–12 days, making deep profile control feasible. Plugging strength increased with concentration; at a 20% concentration, the breakthrough pressure reached 6.72 MPa and the stable pressure reached 6.14 MPa, meeting the strength requirements. The phase-change process was unaffected by the pH and salinity of the on-site water. Core flooding experiments showed that, under injection of 0.3 PV and a 1% mass concentration TSAD system, the plugging rate of high-permeability cores reached 80.69%, while that of low-permeability cores was only 3.1%, and the oil recovery efficiency in low-permeability channels improved by 14.08%, confirming the agent"s effectiveness in plugging fracture channels and enhancing oil recovery. A field pilot test was carried out in well group X-XX of the Chang 6 reservoir in Block W of Wuqi Oilfield. The comprehensive water cut of the well group dropped by 25.85%, and the daily oil production increased from 5.84 t to 7.33 t, achieving a daily oil increment of 1.49 t. This system demonstrates excellent deep profile control performance in fractured low-permeability reservoirs and provides a new idea and effective technical means for water control and enhanced oil recovery.