In situ crosslinked polymer gels (ISCPGs) are widely applied in petroleum reservoirs for conformance control and water shutoff to improve oil recovery. However, the differences in gelation behavior and conformance control performance among ISCPGs formulated with different types of crosslinkers, as well as the underlying microscopic mechanisms, remain insufficiently understood. In this study, the gelation properties of three commonly used crosslinkers—chromium (Cr), phenol-formaldehyde (PF) system, and polyethyleneimine (PEI)—with partially hydrolyzed polyacrylamide (HPAM) were evaluated using the Sydansk bottle-testing method. Core displacement experiments were conducted to compare the injectivity and plugging performance of these ISCPGs in both homogeneous and fractured cores. Results show that Cr-ISCPG had the shortest gelation time (0.3–4 h) and the highest gel strength, reaching grade G, but its long-term thermal stability was relatively poor under reservoir conditions (e.g., 73 °C). PF-ISCPG exhibited superior thermal stability, maintained up to 90 d, but had weaker wall-building capacity compared with Cr-ISCPG. PEI, as a biologically and environmentally friendly crosslinker, yielded PEI-ISCPGs with the longest gelation times and thermal stability, also with the best wall-building performance among the three. In homogeneous cores with gas-measured permeability above 500 × 10−3 μm2, Cr-ISCPG demonstrated strong plugging capability, largely due to its high wall-building strength on rock surfaces. Nuclear magnetic resonance (NMR) analysis provided microscopic insights into ISCPG injection and propagation mechanisms, showing that excessively prolonged gelation time can cause matrix damage. Owing to its stronger wall-building capacity, Cr-ISCPG performed better in plugging highly conductive channels such as fractures, thereby achieving more pronounced conformance control. This work clarified performance differences among ISCPGs crosslinked by different crosslinkers, providing valuable guidance for optimal crosslinker selection and conformance control design in field applications.