Disposal and recycling of heavy metal-enriched biomass is the key to measure the success of phytoremediation. This study employed innovative approach to use Aspergillus niger (A. niger) for the treatment of Cd-contaminated Helianthus annuus L. (sunflower) stalk after phytoremediation. Single-factor results showed that the removal of Cd at an initial pH of 3 was superior to sucrose and inoculation amount. 67.67% of Cd was removed by A. niger leaching system after 11 days based on response surface methodology optimum conditions (sucrose: 76.266 g L−1; inoculation amount: 10%; initial pH: 3), while the concentrations of nitrogen, phosphorus and potassium (N, P and K) of sunflower stalk were unaffected. While physicochemical pretreatment effectively enhanced the bioleaching efficiency, it also resulted in significant loss of P and K elements, thereby reducing the value of biomass for recycling and utilization. Therefore, the direct A. niger leaching method without pretreatment is more advantageous for the safe treatment and recycling of Cd-contaminated sunflower stalks.