Accurate detection of therapy-resistant cancer cell populations remains a major barrier to diagnostic precision and improved patient outcomes. Tumor-initiating cells (TICs), which drive recurrence and metastasis, are difficult to visualize because multidrug resistance transporters limit intracellular probe retention. This study investigated the molecular determinants of TiNIR, a near-infrared probe that targets TICs by binding heme oxygenase 2 (HMOX2). A CRISPR activation screen of 42 ATP-binding cassette (ABC) transporters, integrated with molecular docking and in vivo tumor imaging, identified ABCB1 as the primary efflux transporter regulating TiNIR distribution. These findings demonstrate a dual mechanism of probe selectivity: a binding-dependent pathway mediated by HMOX2 (Holding-Oriented Live-cell Distinction, HOLD) and a transporter-mediated efflux pathway via ABCB1 (Gating-Oriented Live-cell Distinction, GOLD). ABCB1 overexpression reduced TiNIR retention in non-target cells, whereas pharmacological inhibition or gene knockdown restored intracellular accumulation and significantly enhanced tumor signal intensity in mouse xenograft models. Molecular modeling confirmed TiNIR-ABCB1 interactions, supporting transporter-mediated probe clearance. Collectively, these findings establish TiNIR as a dual-mode molecular imaging probe and identify ABCB1 as a key determinant of probe selectivity in heterogeneous tumors. By integrating target binding with transporter efflux, TiNIR enables selective visualization of TICs and provides a framework for designing next-generation probes that overcome resistance-associated barriers in cancer diagnostics and theranostics.