In this work, we developed a drop-type chemiluminescence (CL) system with a partial least squares (PLS) calibration in which the coaxial optical fiber sensing head was developed for sampling and detection to determine Cu²⁺ and Co²⁺ on a silicon wafer directly. The use of time-resolved signal generation and PLS calibration in addition to CL allowed us to determine the metal ions simultaneously and selectively, based on the kinetic difference of Cu and Co ions in the luminol–H₂O₂ system. Two component mixtures with a set of 15 wafer fragments were orthogonally calibrated. After prediction test, the method was applied to an intentionally contaminated silicon wafer and validated by inductively coupled plasma-mass spectrometer (ICP-MS) measurement with a HF–HNO₃ scanning solution. The average concentrations of Cu²⁺ and Co²⁺ of 3.45 (±0.95) × 10¹³ and 2.30 (±1.18) × 10¹¹ atoms per cm², respectively, were obtained, which were very close to the ICP-MS results of 3.70 × 10¹³ for Cu²⁺ and 2.46 × 10¹¹ atoms per cm² for Co²⁺. In conclusion, this drop mode CL showed almost more than 10 times better reproducibility than the typical batch mode for the profile measurement. Moreover, the adoption of PLS calibration added the function of selectivity for the simultaneous determination to this CL system, in addition to the direct mapping capability for the solid surface analysis.