The distribution and bioavailability of dissolved and particulate organic matter (DOM and POM) were determined throughout the water column in sampling transects across the South Yellow Sea (SYS), East China Sea (ECS), and its adjacent Kuroshio Current (KC) during March–April 2017. The carbon (C), nitrogen (N), and amino acids (AA) levels in DOM and POM, as well as other parameters including temperature, salinity, nutrients, chlorophyll-a, and biological parameters (heterotrophic bacteria, Synechococcus, and picoeukaryotes), were used in the multi-factor analysis to explore the underlying factors contributing to the distribution patterns and degrading status of DOM and POM. The AA contents in POM (PAA) were higher at shallower depths than the deep ones, whereas total dissolved amino acids (TDAA) levels showed minor variation with depth. Specifically, glycine and serine in the PAA were selectively preserved throughout the water column. High levels of heterotrophic bacteria were associated with high temperature and high levels of ammonium in shelf waters, indicating a spot for intensive remineralization of organic nitrogen. High concentrations of bulk organic parameters (POC and PON) were found more along the coast and correlated with arginine and alanine. The Kuroshio surface water was short of PAA, POC, and PON compared with the coastal and middle shelf water. The bioavailability of surface POM indicated by the percentages of AA in POC (PAA-C%) and PON (PAA-N%) was much higher in KC than in shelf and coastal waters. This study found the distinctive characterization of bioavailability and degradation status between KC and its adjacent seas.