To improve understanding of the effects of industrial heating processes on its physiochemical and flavour properties, fluid milk was evaluated for protein denaturation and flavour volatiles after high-temperature short-time (HTST), indirect ultra-high temperature (IND-UHT) and direct ultra-high temperature with direct steam infusion (INF-dUHT) treatments. Protein denaturation was evaluated by particle size, free sulphydryl content, fluorescence spectra, native whey protein retention rate and microstructure. Volatile organic compounds (VOCs) were compared by headspace-gas chromatography-ion mobility spectrometry (HS-GC-IMS). HTST treatment exerted the lowest negative effect on the aggregation and denaturation of native whey proteins including α-lactalbumin, β-lactoglobulin and lactoferrin, followed by INF-dUHT. IND-UHT caused the most severe denaturation of native whey proteins. HTST-treated milk was characterised by a high level of low molecular weight ketones and INF-dUHT milk possessed the greatest abundance of aldehydes, whereas IND-UHT milk exhibited the highest contents of high molecular weight methyl ketones, which contributed to an unpleasant aroma.