Whey products have low thermal stability which is decreased when calcium-containing compounds are added to increase calcium content. If calcium is removed from the whey product, thermal stability is improved but its potential for use as a good calcium sources is compromised. The present invention relates to a method for manufacturing a modified whey composition, the method having a liquid preparation step of preparing a raw material whey liquid using an unmodified whey composition containing whey protein without undergoing a calcium reduction treatment, and a heating step of subjecting the raw material whey liquid to a heat treatment, wherein the liquid preparation step includes a treatment of adding an alkali to the whey composition, the pH of the raw material whey liquid is from 6.8 to 8.0 and the protein concentration in the liquid is not more than 1.3% by mass, the calcium content of the raw material whey liquid that is subjected to the heat treatment is from 400 to 700 mg/100 g of solids, and the heat treatment is performed under conditions of 80 to 150°C for a period of 30 minutes to 1 second. The method excludes a calcium reduction treatment during the preparation of the liquid that allows the resulting whey composition to be modified while retaining thermal stability, taste and visual appearance.