This study investigated the genetic variation and genotype–environment interaction (GEI) in the early growth stage among seven full-sib families of the sea urchin Strongylocentrotus intermedius. From each of the seven families, 180 or 270 sea urchins of the same size were exposed to three laboratory environments (E1, E2 and E3). These environments were commonly used in breeding programs for S. intermedius. After a 102 days trial, test height, test diameter, body weight and the coefficient of variation of body weight were determined. The results revealed significant family effects on most growth traits in all the three environments (except for test diameter in environment E2), and significant environmental effects on growth in several families (family 1, 5, 6, 7). The study also revealed that the coefficient of variation in body weight varied significantly among the families (P < 0.01) but not among the environments. Highly significant GEI effects were also recorded for all growth traits (P ≤ 0.001), except for the coefficient of variation in body weight (P > 0.05). Variances of GEI accounted for about 0–2.742% of phenotypic variances for the investigated traits. Significant GEI caused a certain degree family ranking inversions for the growth traits. The present study provides evidence for the existence of GEI in the family selection of sea urchin S. intermedius. More attention should be paid to the GEI to obtain satisfactory genetic gain in S. intermedius.