The invention provides a humic acid chelated boron, magnesium, zinc and iron fertilizer and a preparation method thereof. The fertilizer is composed of the following components in parts by weight: 20 to 30 parts of urea, 10 to 15 parts of diammonium hydrogen phosphate, 10 to 15 parts of potassium sulfate, 30 to 40 parts of boron magnesium slag, 10 to 15 parts of humic acid, 12 to 15 parts of citric acid, 1 to 2 parts of ammonia borate, 6.5 to 8 parts of magnesium sulfate, 7 to 7.5 parts of zinc sulfate, 5 to 6.5 parts of ferrous sulfate, 1 to 2 parts of avermectin, and 0.3 to 0.4 part of diazinon. The preparation method comprises the following steps: preparing medium trace element chelated fertilizer from citric acid, ammonium borate, magnesium sulfate, zinc sulfate, ferrous sulphate and humic acid, then adding urea, diammonium hydrogen phosphate, potassium sulfate, and boron magnesium slag into the fertilizer, grinding, and carrying out a spraying granulation process by using a mixed solution of avermectin and diazinon so as to obtain the finished product. The fertilizer has the advantages of high utilization rate of trace elements, reduction on soil hardening and water pollution, sustain-released effect, and longer lasting drug effect and fertilizing effect.