Carbon quantum dots (CQDs) were successfully prepared via a facile microwave-assisted method combined with a controlled drainage time using glucose as the carbon source. XRD analysis, FT-IR spectroscopy, UV spectroscopy, XPS, and PL spectroscopy were performed to characterize the structures and properties of the samples. The results showed that the average particle size of the prepared CQDs was about 2 nm, and there were two UV absorption at the wavelengths of 228 nm and 280 nm, respectively, corresponding to the π-π* transition of CC (atomic group) and the n-π* transition of the oxygen containing group (CO) on the surface of the carbon core. According to the unique optical and microwave absorption properties of the CQDs, a suitable photocatalytic system, namely, a microwave electrodeless discharge lamp (MEDL) system was used. In the MEDL system, the degradation rate of rhodamine B (RhB, 50 mL, 30 mg L−1) by 0.02 g CQDs-2 in 10 min could reach 85.79%. The photocatalytic activity of CQDs-2 was about twice that of P25. In addition, the biocompatibility of the CQDs was investigated, which revealed that the CQDs could be absorbed by microorganisms as a carbon source. The prepared CQDs are a promising environmentally friendly photocatalyst.