This study investigated a causal association between dietary change and digestive enzyme production of the sea urchin Strongylocentrotus intermedius. Urchins were fed microalgae (Achnanthes longipes, Cocconeis sublittoralis or Saccharina longissima gametophyte), macroalgae (S. longissima sporophyte or Ulva pertusa), or starved, and their growth rate (GR) was examined to identify the size at which sea urchins’ diet shifts from microalgae to macroalgae. Changes in specific activity of seven enzymes (amylase, glycogen hydrolase, carboxymethyl cellulase (CMCase), laminarinase, alginate lyase, protease and lipase) were investigated in urchins of test diameters (TDs) 1.0–3.5, 3.0–4.5 and 6.0–9.2 mm to elucidate ontogenetic and diet-responsive changes. GRs were generally higher in urchins of 3 mm in TD. Our results suggest that the primary nutrient source of S. intermedius shifts from microalgae to macroalgae at ≈6 mm TD, and that macroalgae digestion efficiency in urchins ≥3 mm TD gradually improves because of activation of the enzymes. Highly activated enzymes enable sea urchins to efficiently digest nutrients stored in the bodies of macroalgae, allowing the primary nutrient source of S. intermedius to shift from microalgae to macroalgae.