The analytical method of roller ball pen water inks was established by capillary electrophoresis with photodiode array (PDA) detector scanning in row. First test was for the type, concentration, pH value of buffer solution, as well as the impact of separation voltage of electrophoresis on the analysis results. The test results of PDA detector were studied by fused silica capillaries with diameters of 50, 75 and 100 nm. Experiments show that the capillary diameter is directly proportional to the intensity of light absorption. With ensuring the performance of separation as the premise, using 100 nm diameter of the capillary increased the absorption intensity of signal detection, so the absorption peak can be detected in the range of ultraviolet and visible light wavelength. After optimizing conditions, 20 mmol·L-1 borate buffer at pH 8.5, 100 μm 40 cm fused silica capillary column, separation voltage 15 kV, PDA detector and scanning range 190-600 nm were adopted in experiment. Different roller ball pen inks can be analysed from characteristics of electrophoresis absorption in three-dimensional electrophoregrams with scanning in row in UV-visible wavelength range.