Design, synthesis, and conjugation of mesoporous silica nanoparticles (MSNs) with biomolecules is a matter of growing interest to enhance selective uptake of contrast agents like gadolinium (Gd3+) by cancer cells. Here, by targeting xc-cystine/glutamate antiporter system in breast cancer cells, conjugation of MSN-Gd3+ with cysteine is used to enhance cancer cellular uptake of Gd3+. Reactions designed to make different covalent bonds between MSNs and cysteine to investigate impact of cysteine conjugation of MSNs-Gd3+ on uptake of Gd3+ by breast cancer cells. Cysteine amino acids were attached to the surface of MSNs via its three functional groups using three different conjugation methods. Therefore, the external surface of MSNs were first modified by three different linkers to create amine, epoxy, and isocyanate groups on the surface of MSNs, then pores loaded with Gd3+ complexes and reacted with toile, epoxy, and amine groups of cysteine, respectively (nanoprobe A, B and C). The nanoprobes were characterized using different techniques, including (scanning electron microscope) SEM, Brunauer–Emmett–Teller BET, dynamic light scattering (DLS) and Fourier Transform Infrared (FTIR). The intracellular uptake of nanoprobes by human dermal fibroblasts (HDF) and human breast adenocarcinoma cells (MCF-7) was investigated using inductively coupled plasma atomic emission spectrometer (ICP-AES). Results demonstrated that accumulation of Gd3+ in cancer cells is highly related to method of cysteine conjugation. The amount of Gd3+ was taken by cancer cells increased 7 folds, when thiol group of cysteine was responsible to make covalent bond with MSNs, in other words when the zwitterionic form of cysteine was on the surface (nanoprobe B). The average intracellular uptake of Gd3+ by cancer cells was 0.5±0.09 pg/cell. On the other hand, uptake of Gd3+ delivered by nanoprobe B into cancer cells was up to 4.7 times higher than normal cells. No appreciable cytotoxicity was seen using HDF and MCF-7 cell lines. This study provides MRI nanoprobes using suitable conjugation of Gd3+ based MSNs with cysteine for next studies about MR imaging of cancer.