Abstract: Possible causes for poorer regeneration of indica variety 9311 than japonica variety Nipponbare were analized by comparing the differences of physiological metabolism in callus, which obtained at different stages of callus induction and differentiation. The results demonstrate that, in different culture days of callus induction and differentiation, total nitrogen and ammoniacal nitrogen in Nipponbare callus is higher than that of 9311. Nitrate nitrogen in Nipponbare is also higher than that in 9311 before 25days of callus differentiation. Moreover, at the level of cells metabolism, soluble protein in Nipponbare is higher than that in 9311 from callus induction to 15 days of differentiation.