Since microwave irradiation could promote hydrolysis and olation of chromium tanning liquor, but the influence of microwave on chromium complex component in the liquor was still unknown. Chromium sulphate solution (0% basicity) and 33% basicity chromium tanning liquor were subjected microwave (MW) and water bath (WB) heating, and the samples without any warming were regarded as control. Ion exchange chromatography (IEC) and gel filtration chromatography (GFC) were used to measure the charge composition and molecular size of chromium complexes in each sample. FT-IR was used to characterize the structure of chromium complexes in each composition separated by IEC. Moreover, the chromium tanning liquor after warming was used in hide powder tanning trials to illustrate whether microwave would affect its tanning ability. The results show there are more high positive charge and large molecular size complexes in chromium tanning liquor after warming but the phenomena are more significant in MW samples compared with WB due to non-thermal effect of microwave. In addition, microwave has more powerful effect on 33% basicity chromium tanning liquor hydrolysis and olation to generate larger molecular size complexes. In FT-IR results, the combination pattern between chromium and ligands are changed after warming but there is no difference between WB and MW. The chromium exhaustion and thermal stability of hide powder tanned with chromium tanning liquor after microwave irradiation are both higher. It could conclude that both thermal and non-thermal effects of microwave promote the process together, and the nonthermal effect leads to more high positive charge and large molecular size complexes and has stronger influence on high polarity system. In short, this work would provide theoretical basis for applying microwave in tanning agent modification and chrome tanning process further.