The processes of gametogenesis, development, and degeneration, together with the gonad fatty acids, of the pen shell Atrina pectinata were studied. The results showed that water temperature is the key factor affecting gonadal development. The gonad started to develop and differentiate at 6–7°C, with fast development of both the visceral mass and the gonad when the temperature increased to 11–12°C. The gonad index peaked at approximately 21°C, which suggested that 6–7°C is the threshold for gonad development and that 21°C is the optimum temperature at which broodstock will mature. The gonad fatty acid 18:1n-9 correlated remarkably with the condition and gonad indices, which might be indicative of the maturity of the gonad of A. pectinata. From the perspective of nutritional composition, Pavlova sp. and Chroococcus sp. were thought to be the most appropriate feed for A. pectinata broodstock cultivation.