High-concentration antibiotics are detected in surface water from time to time. There has been an increasing demand for strengthening the supervision of the antibiotic pharmaceutical wastewater. Three-dimensional fluorescence technique is known as a rapid, simple and high-sensitivity method. The three-dimensional fluorescence spectrum can display organic components and it was named as aqueous fingerprint. In this paper, three-dimensional fluorescence characteristics of a typical semi synthetic penicillin pharmaceutical wastewater were studied. There were totally four fluorescence peaks in the aqueous fingerprint of this wastewater, locating in excitation wavelength/emission wavelength of 360/445, 255/445, 275/305 and 230/300 nm respectively. Fluorescence peak’s intensity within certain range related linearly to the relative concentration. The possible fluorescent pollutants related to Peak C and Peak D might be the mixture of D-(-)-A-4-Hydroxyphenylglycine Dane Salt Methyl Potassium (pharmaceutical intermediates), Amoxicillin (pharmaceutical product) and D(-)-4-Hydroxyphenylglycine (pharmaceutical hydrolysate). PH played an important role in the fluorescence characteristics of this wastewater. This indicated that the fluorescent organic pollutants in this wastewater might contain acid or base groups. The aqueous fingerprint technique could be used to monitor the discharge of semi synthetic penicillin pharmaceutical wastewater as a novel tool.