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Flow injection analysis was adopted for the determination of trace element in seawater samples, and the relative instrument was developed. Based on the FCS design ideas, a software-hardware integration measurement platform with automated adaptive external devices, rapid formation of a variety of instruments and all-digital communications had been established. The platform was embedded with ARM (S3C2416) processor and Linux operating system, which had a human-computer interaction by LCD and an input-controller by touch screen or USB mouse. It used a CAN bus and developed a CAN Application Layer (CAL) protocol for device management. It showed characteristics of automation, versatility, reusability and scalability to achieve analysis of trace nitrite, nitrate, ammonia, phosphorus, iron and other elements in seawater, in laboratory, shipboard and in-situ applications. In the practical test, the measurement results of the platform had no significant differences with that of a commercial special spectrophotometer.