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On the basis of a multiple linear regression model performed for ionospheric NmF2, partial correlation method is first applied to investigating the relation between NmF2 and h (the height of isobaric level) in the lower atmosphere over Wuhan, China during 1957―2004. The results show that partial correlation method can eliminate the influences of solar and geomagnetic activities as well as the seasonal variation factors and reveal the true correlation between NmF2 and h in the lower atmosphere. A weak positive correlation between NmF2 and h is found in the middle stratosphere. In addition, by comparing the partial correlation coefficients between NmF2 and its influence factors, we find that NmF2 is mainly affected by solar activity and the seasonal variation factors, and weakly affected by geomagnetic activity, but hardly affected by h in the lower atmosphere. The study suggests that partial correlation method is a helpful tool for investigating the correlation between ionospheric parameter and its influence factors.