In this study, we conducted a novel approach of selective breeding by using temperature acclimation to enhance the aquaculture potential of the tropical cyclopoid copepod Apocyclops royi. Two copepod culture strains were acclimated separately at high (28°C, control strain) and low (18°C, selective strain) temperature for 10 months, corresponding to ~40 and 15 generations, respectively. After temperature acclimation, multigenerational observations were made to investigate the effects of cold selection on the copepods. Differences in female and nauplius lengths, nauplius production, and fatty acid contents were evaluated between the control and selective strains before (F0) and during the multigenerational observation (F1–F4). Overall, the selective strain exhibited larger females, higher nauplius production, but smaller nauplii than the control strain did. In generation F1, the total fatty acid and omega 6 and omega 3 polyunsaturated fatty acid contents were higher in the selective strain than in the control strain; however, the fatty acid content gradually decreased in subsequent generations. This paper reports the effects of temperature acclimation on the morphological and physiological traits of A. royi and provides preliminary suggestions for improving its productivity and nutritional value as “designer feed” for aquaculture applications.