Capillary electrophoresis (CE) has proven to be an effective technique for aptamer selection. Here, we directly integrated the separation advantages of CE into a live-cell system, thereby establishing an integrated and highly efficient CE-Cell-SELEX screening model for bone microvascular endothelial cells (BMECs) without the need for negative selection. The selection progress was monitored through quantitative real-time fluorescence PCR (qRT-PCR) analysis, which yielded 7 candidate sequences from the amplified library after four rounds of selection. Flow cytometry analysis demonstrated that aptamer T-24 exhibited high affinity for BMECs, with a Kd of 111.86 ± 18.36 nM. Owing to its high affinity and specificity, coupled with its small molecular weight and non-immunogenicity, T-24 holds great potential as a biological probe for the identification and isolation of BMECs. Furthermore, molecular docking was performed by MOE 2022 software to validate the candidate sequences and assist in the identification process. The CE-Cell-SELEX method eliminates the need for negative screening and traditional elution, greatly reduces the screening cycle, and may provide a valuable reference system for the early diagnosis and precise treatment of femoral head ischemia.