Hexamethylene-1,3-bis(cetyldimethylammonium bromide) (G 16-6-16) protected low-toxicity ZnSe quantum dots (QDs) were successfully synthesised and used as fluorescence probe to detect proteins such as bovine serum albumin (BSA). This method is simple, fast, selective and sensitive. Surfactant G 16-6-16 can interact with proteins through hydrophobic effect, thus leading to the fluorescence quenching of G 16-6-16 protected ZnSe QDs nanometre material. The fluorescence intensity of G 16-6-16 protected ZnSe QDs was linearly proportional to BSA over a concentration range from 0 to 80 nM with a correlation coefficient of 0.993. The detection limit was 0.04 nM. This method was successfully applied to determine BSA in urine samples which shows the good application value of this nanometre material.