The invention discloses an azadirachtin fertilizer and application thereof in improvement on the content of squalene in tobacco leaves. The azadirachtin fertilizer is prepared from the following components: 30 to 60 percent of azadirachta indica seed and the balance of diatomite. The azadirachtin fertilizer is applied in a growth process of tobacco, so the content of the squalene in the tobacco leaves can be remarkably improved, and economic value of the tobacco leaves is improved.