In this work, electron beam lithography proximity effect correction (PEC) was experimentally studied for patterning of Si photonic waveguides with a relatively thick resist mask. Beam’s energy density distribution (EDD) was experimentally extracted by the line exposure method; however, exposure lines in this work were developed after cleavage with a high-contrast process to reduce developer-related effects. The measured line spread function was fitted to a 4-Gaussian function to model mid-range energy densities accurately. The extracted EDD showed less proximity effects compared to conventional Monte-Carlo simulation performed by a commercial software. PEC processes with both techniques were experimentally compared for a Si photonic waveguide pattern with different side-cladding trench widths. Microscopic images confirmed that the presented calibration method could achieve better development conditions near the required clearance dosage. Single-mode propagation loss for a 500 × 220 nm Si wire waveguide was reduced from 3.2 to 2.4 dB cm−1 using the presented process.