Strontium-90, a highly radioactive isotope, accumulates within the food chain and skeletal structure, posing significant risks to human health. There is a critical need for a sensitive detection strategy for Strontium-90 in complex environmental samples. Here, solid-state nanochannels, modified with metal-organic frameworks (MOF) and specific aptamers, were engineered for highly sensitive detection of strontium ion (Sr2+). The synergistic effect between the reduced effective diameter of the nanochannels due to MOF and the specific binding of Sr2+ by aptamers amplifies the difference in ionic current signals, enhancing detection sensitivity significantly. The MOF-modified nanochannels exhibit highly sensitive detection of Sr2+, with a limit of detection (LOD) being 0.03 nmol·L–1, whereas the LOD for anodized aluminum oxide (AAO) without the modified MOF nanosheets is only 1000 nmol·L–1. These findings indicate that the LOD of Sr2+ detected by the MOF-modified nanochannels is approximately 33,000 times higher than that by the nanochannels without MOF modification. Additionally, the highly reliable detection of Sr2+ in various water samples was achieved, with a recovery rate ranging from 94.00% to 118.70%. This study provides valuable insights into the rapidly advancing field of advanced nanochannel-based sensors and their diverse applications for analyzing complex samples, including environmental contaminant detection, food analysis, medical diagnostics, and more.