The manufacturing process efficiencies and the products quality of herbal medicine often suffer from high variability with the variability of the raw materials. This paper presents a methodology for adjusting process parameters according to the raw materials variation for acceptable adsorption efficiencies during HM column chromatography process. The methodology was illustrated by an example of saponins adsorption process, which is a critical unit operation in macroporous resin column chromatography during Panax notoginseng injection manufacturing process. The impact of total saponins concentration in loading solution and adsorption time on adsorption efficiencies was mapped. The specification region of raw material was obtained and the adsorption efficiencies at the end of the adsorption process were predicted early-on. When the predicted adsorption efficiencies did not meet the target values, the control method proposed the use of an adjusted process parameter leading the adsorption process towards the target adsorption efficiencies at the end of the adsorption process. The results in this work facilitated the enhanced understanding of the relationships between raw material attributes, process parameters and saponins adsorption efficiencies. This case study demonstrated that it is possible to employ different process parameters to accommodate raw materials variation for acceptable process efficiencies. (c) 2013 Elsevier B.V. All rights reserved.