In order to explore the effects of PPMn type water soluble fertilizer mixed with humic acid of cottonseed meal fertilizer on soil properties and cotton yield, the functional and appearance characteristics of two novel water soluble fertilizers were studied by infrared spectroscopy and scanning electron microscopy analysis. The field experiments were also conducted to study soil physical properties, cotton yields and fertilizer use efficiency. The results showed that application of humic acid fertilizer of cottonseed meal (H), PPMn type water soluble fertilizer (P) and two new types of water soluble fertilizer (HP) had the better effects on improving soil physicochemical structure and enhance the cotton yield than the conventional water soluble fertilizer (S) and no fertilizer (CK), and HP gave the best. Under HP, soil bulk density was decreased by 8.15%, soil porosity was increased by 7.49%, the proportion of <0.25 mm soil aggregate was reduced effectively, the agronomic efficiency of nitrogen phosphorus and potassium was improved significantly, and the cotton yield was increased by 7.5%~41.0% compared with other treatments.