The effects of organic and inorganic N combined application on P.notoginseng cultivation are poorly known. For this reason, we have carried out a pot culture experiment in 2010. The treatments respectively were (1) control (no N input, CK), (2) organic N (ON), (3) half organic N and half inorganic N (1/2ON+ 1/2IN), (4) inorganic N (IN). Plant growth, NPK and secondary metabolites concentration were assayed. Results showed that compared to CK, ON increased plant height, N, P concentration and accumulation and total saponins concentration, but reduce total flavonoids concentration. IN increased shoot and root biomass, N concentration and accumulation, K accumulation, but reduce total flavonoids and saponins concentration. 1/2ON+ 1/2IN had the highest hair root length, root diameter, biomass, N concentration and accumulation, K concentration in roots, total saponins concentration, but had the lowest K concentration in shoots, total flavonoids concentration in shoots and roots. Correlation analysis showed total flavonoids concentration was negative correlated with N concentration and accumulation, K concentration in shoots, but was positive correlated K concentration in roots. Total saponins concentration was negative correlated with K concentration in shoots whereas positive in roots, and was negative correlated with total flavonoids concentration. Totally, organic and inorganic N combined application with the ratio of 50/50 is the best way for growth and saponins of P.notoginseng.