The invention discloses a modified sodium lignin sulfonate chelating agent containing a phosphonic acid group and a preparation method thereof. The preparation method comprises the following steps: preparing 30-40 mass percent of aqueous solution from sodium lignin sulfonate powder; adding a phenolic substance, regulating the pH value of the system to 8-10, and reacting at the temperature of 90-100 DEG C for 0.5-1 hour by adopting the microwave power of 300-1200W; taking out the reaction solution, adding epoxy chloropropane and short-chain alkyl polyamine, heating in a normal pressure water bath, and reacting at the temperature of 70-80 DEG C for 1-2 hours; cooling to the temperature of 30-40 DEG C, adding a phosphorous acid crystal, and uniformly stirring and mixing; and cooling to the temperature of 30-40 DEG C, dripping a formaldehyde solution, heating to the temperature of 80-100 DEG C, and reacting for 2-4 hours, thereby obtaining the modified sodium lignin sulfonate chelating agent. The chelating agent molecule contains lots of hydroxyl radicals, carboxyl, amido and phosphonic acid groups, can form compound coordination with zinc, copper, lead, nickel and other divalent metal ions and has high chelating ability.