During October 2005 to October 2006, the annual variations of the primary productivity (PP) of phytoplankton and its size-fractioned structure in the culture ponds of Apostichopus japonicus Selenka were investigated on the coast of North Yellow Sea, Dalian, Liaoning Province of China. This study aimed to determine the basic ecological characteristics in culture ponds of A. japonicus, provide scientific supports for production and management of A. japonicus culture. The mean area of the experimental ponds was 3.0 hm² with mean water depth as 1.8 m. Mean seeding density of cultured animals and seed size in the ponds were 49829 ind./hm² and 1.25 g/ind. During the experiment seawater temperature varied from -1.4 to 26.5 ℃, salinity 25.5 to 34.5‰, pH 7.56 to 8.23, transparency 0.2 to 1.8 m and annual mean value of NH₄⁺-N was (0.05 ± 0.03) mg/L. PP was estimated by dark and light bottles method. The depths of suspending bottles were generally 20 cm (surface layer), 0.5 ×, 1 × and 2 × of transparency, time of suspending bottles was 10:00-14:00, the amount of dissolved oxygen was determined by Winkler method, then PP in the whole day was calculated according to the results. Determination of size-fractioned structure of PP: Water samples were filtered by 200 μm sieve silk, 20 μm, 2 μm and 0.2 μm filter membrance, then the raw water and fractionated water samples were placed into dark and light bottles to suspend at the surface layer in the middle of each pond. Time of suspending bottles and determination method of dissolved oxygen were as same as PP experiment. The subtraction method was used to calculate PP of different size-fractioned phytoplanktons, while hydrochemical parameters were measured by Chinese national standards. The results showed that the annual mean value of PP was (5.16 ± 3.04) gO₂ m^-2 d^-1 in the culture ponds, which obviously presented seasonal variations. PP reached peaks in early spring, summer and early winter, respectively. The percentage that net production of community in gross production of PP was 50.2%. The annual mean values of P/R value and daily P/B ratio were (2.20 ± 1.25) and (0.39 ± 0.35). According to the nutrient types of water which was determined by the level of PP and P/R value, the experimental ponds were eutrophic water. PP decreased with the increase of water depths. The water layer of highest production was approximately at the depth of 0.5 times of transparency. PP above 0.5 times of transparency (about 50 cm) accounted for 56.3% in total production of water column. The percentages of productions of different size-fractioned phytoplanktons in total production presented obvious seasonal variations. The contribution of micro-phytoplankton (20-200 μm) to PP was the largest (43.5%) except in summer. In summer, the largest part to PP was contributed by nano-phytoplankton (2-20 μm) (35.3%). The percentages of PP of different size-fractioned phytoplanktons in total prodution that were ordered as: micro- (40.1%) > nano- (28.2%) > meso-macro (16.1%) > pico- (15.7%). Regression analysis showed that PP in the experimental ponds with water temperature, NH₄⁺-N, NO₂^--N were of significant correlation (P < 0.05), respectively. The results indicated that the seasonal variation of PP was obvious, which vertical distribution was not uniform, micro-phytoplankton was the main producer in a culture pond of A. japonicus.