The invention discloses a fertilizer with kieselguhr and a preparation method and use method thereof. The fertilizer, 100 parts in total, is prepared from, by weight, 0-30 parts of nitrogen element, 0-20 parts of phosphorus element, 0-30 parts of potassium element, 0.3-30 parts of kieselguhr and the balance filler. Kieselguhr has the nanometer granularity. The method includes the step of conducting nanometer treatment on kieselguhr and the step of mixing nanometer kieselguhr with other components. The fertilizer can be used in a bottom application mode or a dressing mode or a crop leaf surface spraying mode. The fertilizer is high in utilization rate, environmentally friendly and capable of reducing soil hardening. The preparation method is simple in process, low in device requirement and capable of saving energy consumption and reducing cost.