Aptamers have presented considerable potential for disease diagnoses but still face a great challenge from the discrepancy between their screening conditions and real application in body fluid matrices (BFMs). In this study, we investigated the impact of BFM intervention on aptamer screening based on CE efficient separation and introduced adaptive screening strategies directly under the BFM background. Five BFMs, including serum, tears, artificial cerebrospinal fluid, saliva, and embryonic fluid, demonstrated the potential differentiating effects on aptamer screening based on the characterization of their "fingerprint-like profile" and their interactions with ssDNA libraries. Besides, the matrix effects of the five BFMs were quantified by calculating kinetic parameters derived from binding investigations between disease marker protein-spiked BFMs and ssDNA libraries. Through quantitative evaluation, two tailored SELEX strategies were introduced in BFM-intervened aptamer screening: spiking foreign proteins to the BFMs, and targeting proteins naturally abundant in BFMs. As proof of concept, we completed aptamer screenings for prolactin-induced protein (serum, spiked target) and human lactoferrin (tears, natural target) via CE-SELEX that demonstrated its adaptability in "splitting" BFM interference and achieving a clear collection of target-ssDNA complex. This study highlighted the critical importance of incorporating BFMs into SELEX and provided two tailored strategies that are worthy of choice for effective aptamer discovery, advancing the practical utility of aptamers.