Heteroatom doping is a valid strategy for improving the lithium/sodium storage capacity of carbon materials. Here, N-doped hierarchical porous carbon (NHPC) with defects is designed and synthesized via a low-cost and green synthesis method using lignite humic acid extraction residue as the raw material. Through experiments and theoretical calculations, the effects of N-doping and defects on Li+/Na+ storage capacity are systematically analyzed. With the introduction of defects and N atoms, electrical conductivity, and Na+ adsorption energy of NHPC gain improvement. The porous structure could shorten the Li+/Na+ diffusion path and relieve the volume dilation and mechanical strain. Compared with other counterparts, NHPC obtained at 700 °C maintains a bigger reversible capacity of 940 mAh/g at 0.1 A/g in lithium-ion batteries. Even at 1.0 A/g, the specific capacity of NHPC-700 stabilizes at 508 mAh/g with a capacity recession of only 0.021% per cycle after 1000 cycles. In sodium-ion batteries, NHPC-700 anode also exhibits a high specific capacity (320 mAh/g at 0.1 A/g) and good cycling stability (225 mAh/g after 1200 cycles at 1.0 A/g). Here, the entire synthesis route is an eco-friendly process, which achieves zero discharge and zero pollution.