The invention discloses a water body nutritive salt in-situ detection instrument and method based on an integrated valve island apparatus. The water body nutritive salt in-situ detection instrument comprises an integrated valve island, a peristaltic pump, a heater, an optical circulating pond, an LED (Light-Emitting Diode) lamp, a photoelectric acquiring module and a computer processing module. The invention also provides a method for online detecting seawater nutritive salt by using the seawater nutritive salt in-situ detection instrument. The nutritive salt in-situ detection instrument disclosed by the invention is based on the valve island apparatus, completes selectively sample feeding and mixing on the valve island apparatus, is high in integration degree and small volume, and is suitable for online analysis. The nutritive salt in-situ detection instrument is capable of completing determination of multiple kinds of nutritive salts under the drive of the single peristaltic pump, is low in energy consumption, and is conveniently applied to an in-situ sensor. According to the nutritive salt in-situ detection instrument and method, through a three-way valve and a parallel heating reaction coil, the influence of an external environmental condition to a determination result is reduced, the reaction temperature and chemical color-developing time are increased, thus the reaction progress is increased and the analysis sensitivity is improved.