Ultra-fine fibers derived from sea-island fibers have attracted great attention due to their excellent overall performance. However, green and efficient splitting of sea-island fibers is still a challenging task. In this work, thermoplastic polyvinyl alcohol (TPVA) was prepared by the physical blending of plasticizer. The modified TPVA showed a high decomposition temperature (285 °C) and a wide thermoplastic processing window. This made TPVA match well with polyamide 6 (PA6) to form conjugated melts at 250 °C. Corresponding PVA/PA6 sea-island fibers were first reported to realize water-splitting instead of alkali-extraction of “sea” polymers. The effects of sea/island mass ratios and different spinning speeds on the properties of PVA/PA6 sea-island pre-oriented yarn (POY) were investigated. A higher spinning speed enhanced the orientation-induced crystalline behavior of fiber, therefore increasing the tensile strength of fibers. As the increase of spinning speed from 1000 to 1500 m/min, the crystalline degree of corresponding POYs increased from 9.9 to 14.3%. The plasticizer in PVA did not diffuse to the PA matrix during spinning. However, PVA could induce the crystallization of PA6 via interfacial hydrogen bonding. When the spinning speed was 1500 m/min, and PVA/PA6 was 7:3, the tensile strength reached the highest value of 1.67 cN/dtex. The uniform diameters of ultra-fine PA6 fibers (2–5 μm) were obtained by an environment-friendly water-splitting process. The “sea” phase (TPVA) in sea-island fiber could be removed quickly by boiling water treatment in 3 min. This green and energy-saving sea-island fiber splitting technique is of great significance in reducing CO2emissions during the preparation of super-fine fibers.