A study was conducted to determine effects of reducing hindgut pH through dietary inclusion of high-amylose cornstarch (HA-starch) on growth performance, organ weights relative to live body weight (BW), blood thyroid hormone levels, and glucosinolate degradation products of nursery pigs fed cold-pressed canola cake (CPCC). A total of 240 pigs (initial BW: 7.1 kg), which had been weaned at 21 d of age, were housed in 40 pens (6 pigs per pen) and fed 4 diets (10 pens per diet) in a randomized complete block design for 28 d. Four diets were a basal diet with CPCC at 0 or 40%, and with HA-starch at 0 or 40% in a 2 × 2 factorial arrangement. The diets were fed in two phases: Phase 1 from day 0 to 14 and Phase 2 from day 14 to 28 and were formulated to have the same net energy, standardized ileal digestible AA, Ca, and standardized total tract digestible P contents. Dietary inclusion of CPCC and HA-starch was achieved by a partial or complete replacement of corn, soybean meal, and soy protein. At the end of the study, one pig from each pen was euthanized to determine organ weights, blood parameters, hindgut pH, and glucosinolate degradation products. Dietary CPCC reduced (P < 0.05) overall average daily gain (ADG) by 15%; increased (P < 0.05) relative weights of liver and thyroid gland by 27% and 64%, respectively; and reduced (P < 0.05) serum tetraiodothyronine (T4) level from 30.3 to 17.8 ng/mL. Heart, kidney, and gastrointestinal tract weights; serum triiodothyronine level; and hindgut pH of pigs were unaffected by dietary CPCC. Dietary HA-starch reduced (P < 0.05) overall ADG, relative weight of thyroid gland, cecal, and colonic pH; but increased (P < 0.05) relative weight of colon; tended to increase (P = 0.062) serum T4 level. Dietary CPCC and HA-starch interacted (P = 0.024) on relative weight of thyroid gland such that dietary CPCC increased (P < 0.05) weight of thyroid gland for HA-starch-free diet (120 vs. 197 mg/kg of BW) but not for HA-starch-containing diet (104 vs. 130 mg/kg of BW). Dietary CPCC and HA-starch interacted (P = 0.001) on cecal isothiocyanate content such that dietary CPCC increased (P < 0.05) level of isothiocyanates for HA-starch-containing diet but not for HA-starch-free diet. In conclusion, dietary CPCC reduced growth performance, increased liver, size and interfered with thyroid gland functions of pigs. However, the negative effects of dietary CPCC on thyroid gland functions of nursery pigs were alleviated by dietary HA-starch.