Rapid analysis of metabolites in biofluids is of great importance for disease diagnosis or new-born disease screening. Herein, we introduce an agarose hydrogel conditioning method to enhance the performance of paper spray ionization mass spectrometry. With facile and fast hydrogel conditioning, the signal intensity of therapeutic drugs spiked in urine was 5 to 15 fold higher than that in direct paper spray ionization mass spectrometry analysis. Consequently, the sensitivity of metabolites in urine was improved via hydrogel conditioning, resulting in 9 to 15 fold decrease in the possibility of detection (POD) levels. These results show that agarose hydrogel conditioning coupled with paper spray ionization mass spectrometry could serve as a facile ionization method for ambient mass spectrometry, which might be useful in fast screening of metabolites and therapeutic drugs in raw biofluids.