The invention provides an off-site treatment method and system for mud polluted by heavy metals in a river. The method comprises the following steps of: (1) conveying dug bottom mud to the bank, washing off pebble, macadam and coarse sand, and performing thermal refining treatment on the bottom mud containing a leacheate; (2) performing mud and water separation on the bottom mud subjected to the thermal refining treatment; (3), sieving mud fluid subjected to the mud and water separation, and sieving out medium-fine sand; (4) removing coarse mud from the undersized mud fluid; (5) performing mud and water separation on the mud fluid, and conditioning the bottom mud with relatively high concentration by use of a flocculant; (6) dewatering the conditioned mud fluid; (7)mixing and stirring the dewatered bottom mud and a stabilizer solution, and performing stable consolidation treatment. The system comprises a roller stone washer, a mud collection pool, a spiral sand washer, a mud fluid mixing and conditioning pool, a mud fluid precipitation pool, a vibrating sieve, a hydraulic swirler, a mud fluid condensation pool, a mud fluid conditioning pool, mechanical dewatering equipment and stable consolidation stirring equipment. The method and the system are convenient to implement and operate, good in treatment effect and free from secondary pollution.