We proposed a green microwave-assisted hydrothermal way to synthesize highly crystalized N-doped carbon quantum dots(N-CQDs). The N-CQDs obtained by this microwave method have good crystalline degree(I-D/I-G=0.6) and a high molar ratio of N/C(11.1%) comparing with those obtained from traditional top-down method. The experimental results show that glycerine plays a key role in the formation of highly crystalized N-CQDs. The as-prepared N-CQDs have good luminescent property and may be utilized as fluorescent probe to detect ions or mark cells. As the majority of N atoms in the N-CQDs were pyridinic type(64.8%), the as-prepared N-CQDs were used as a catalyst for the oxygen reduction reaction(ORR) electrocatalysis in the anode of the fuel cell(the onset potential is -0.121 V), which was a 4e-transfer procedure and the catalyst showed good stability after 100 cycles.