In this paper, with the observed critical frequencies of F2 layer at Kokubunji （139.5°E,35.5°N） during 1959 to 2004, the dependence of the variations of NmF2 on the geomagnetic activity, solar activity, season and local time are statistically investigated. The results show that there are more positive ionospheric storm effects than negative ones over KokuSunji. In summer, negative storm effects prevail during high solar activity, whereas positive storm effects are usually observed during low solar activity; in winter, positive storm effects dominate regardless of solar activity conditions; and in equinox, negative storm effects with smaller amplitude are often seen during high solar activity, and positive storm effects often take place during low solar activity conditions. The correlation analysis between the disturbance of NmF2 and ap index also illustrates the above-mentioned feature. Furthermore, our results show that there is a time delay of 12-15 hours between the ionospheric maximum negative disturbances and the maximum geomagnetic perturbation, and the time delay of the ionospheric positive disturbances are 3 and 10 hours, respectively. In addition, it is also found that under high geomagnetic activity conditions, positive disturbances are often seen in the evening, and negative disturbances in the morning.