As an essential trace element, abnormal levels of copper ions (Cu2+) in body are associated with various disease. Various methods have been developed for Cu2+ sensing, but the construction of portable sensors for online and sensitive detection of Cu2+ in complex samples is still urgent. In this work, a portable and in-situ optical fiber fluorescent sensor was firstly operated by combining tapered optical fiber and fluorescent silicon quantum dots (SiQDs) via hydrogel strategy and used for ultrasensitive detection of Cu2+ in serum. The hydrothermally synthesized SiQDs of blue fluorescence exhibited excellent specificity of response to Cu2+ due to the static quenching effect. Good linear correlations were obtained over Cu2+ concentration from 0.01 to 50 μM. The sensor was successfully used for rapid detection of Cu2+ in serum samples avoiding tedious pretreatment. The sensor provided a portable and effective platform for online and ultrasensitive determination of Cu2+ in complex samples with the detection limit of 3.58 nM, as well as promising for the detection of biomolecule mediated by Cu2+. This method demonstrated superiority in high sensitivity and selectivity, convenient practicability and easy fabrication. It is of significance for the analysis in narrow space, remote sensing and emergency analysis.