To clarify the effects of malonyl ginsenosides (MGR) on evaluation and quality control of Panax ginseng, the contents of neutral and malonyl ginsenosides from P. ginseng were examined by high-performance liquid chromatography equipped with UV-VIS detector (HPLC-UV) during extraction, processing and storage. Several solvents, including water, ethanol, methanol, and n-butanol were used in the cold-soaked extraction (CSE). Among the four extraction solvents, methanol was found to be the most efficient. CSE was compared with other extraction methods such as Soxhlet extraction (SE), heat reflux extraction (HRE), ultrasonic-assisted extraction (UAE), and microwave-assisted extraction (MAE). The content of MGR showed significant differences, higher in CSE and UAE; lower in MAE and HRE; no MGR could be detected after SE. However, the total contents of neutral and malonyl ginsenosides were not different. Meanwhile, white ginseng, stored at 25°C in air of low humidity, showed a marked decrease in the concentration of MGR from 1.19% to 0.63% but with an increase in the neutral ginsenosides from 1.12% to 1.53% after 0-9-month storage. The results indicated that MGR changed dynamically in P. ginseng with different extraction solvents, extraction methods and increasing storage time. The total ginsenosides was not only underestimated but also determined imprecisely by ignoring malonyl ginsenosides. On the basis of our results, we suggest that malonyl ginsenosides should be transformed into the corresponding neutral ginsenosides during sample preparation for quality control and evaluation of P. ginseng. Then the content of six neutral ginsenosides in samples was used as the true level of total ginsenosides. The results reported here might provide useful information for accurate evaluation and quality control of P. ginseng.