A simple, rapid, and green high-performance liquid chromatography-mass spectrometry (HPLC-MS) method was developed for determination of tauroursodeoxycholic acid (TUDCA), taurocholic acid (TCA), and taurochenodeoxycholic acid (TCDCA) in bio-transformed Jindanfen (BTJDF), which is obtained from chicken bile through a bioconversion process. The sample was prepared using water. The HPLC separation was operated on a poroshell 120 EC-C18 column with a 2.0 min gradient elution procedure. Detection was performed on a single quadrupole mass spectrometer in negative mode with selected ion monitoring mode (SIM). This developed HPLC-MS method presented good linearity (r > 0.997) and sensitivity (limit of quantification, 30.0–80.0 pg) for three analytes. The relative standard deviations (RSDs) for precision, repeatability, and stability were all below 3.00%. The matrix effects and average recoveries of three analytes were 91.2–97.9% (RSDs < 1.50%) and 95.4–103% (RSDs < 3.00%), respectively. The average contents of TUDCA, TCA, and TCDCA in ten batches of samples were 33.8, 13.2, and 20.5%, respectively. Finally, the greenness of the developed method was validated by Analytical Eco-Scale and Complex-GAPI. The developed method was proved to be an eco-friendly, effective, and reliable approach for assaying the three cholic acids in BTJDF, which is help to improve the quality evaluation level of the BTJDF industry.