The hydroxyl polyacrylate emulsions (HPAE) for waterborne two-component polyurethane coatings (WB 2K-PUR) were synthesized by semi-continuous seeded emulsion polymerizations with trihydroxymethyl propane triacrylate (TMPTA) used as an inner cross-linking agent added by multi-stage. The effects of the TMPTA amounts and distributions in core/shell parts of latexes on the emulsion polymerization stability and the film properties were studied. The results indicated that the WB 2K-PUR film with 2 wt% TMPTA displays excellent physical-chemical properties including 0.78 of hardness, 96.4% of cross-linkage degree and 92% of gloss, besides good emulsion polymerization stability with 0.26% of coagulation contents. TGA curves indicated that WB 2K-PUR film with 3:7 of the TMPTA distribution ratio in the core and shell parts exhibits good thermal stability.