In the field of nuclear technology applications, digital multi-channel pulse amplitude analysis technology plays an indispensable role in information acquisition due to its high precision and sensitivity. However, the challenge of pulse pileup can compromise the accuracy of measurement results in this technology. While conventional filter shaping and pulse pileup processing methods can extract nuclear pulse feature information under mild pileup conditions, severe pileup can notably degrade spectral counting rate and resolution. This paper introduces a designed two-channel pulse pileup rejection method, termed the cusp-flattop hybrid filter forming algorithm, leveraging the unique features of cusp, such as high forming speed and minimal interference from pulse pileup. The two channels simultaneously process the collected signals and utilize their differences for data filtering and rejection. This approach enhances information content, improves data processing quality, and boosts the signal-to-noise ratio. Compared to three methods—three trapezoidal filter shaping algorithms, the triangle trapezoidal pulse shaping algorithm, and the pulse width discrimination algorithm—our proposed method refines the shaping threshold of pulse pileup rejection. It accurately distinguishes and extracts effective pulse amplitudes even under severe pileup conditions, generating energy spectrum results while accounting for counting rate and resolution. Building on this, we construct a digital multichannel pulse amplitude analysis system based on FPGA (Field Programmable Gate Array) and use a national standard alloy sample, YSBS41346, for testing. The system can generate energy spectrum correctly, consistent with the actual sample content. We evaluate the system's performance by comparing the peak counting rate and resolution of the energy spectrum generated by the cusp-flattop hybrid filter forming algorithm and the trapezoidal forming algorithm. A high peak counting rate represents the maximum nuclear pulse data captured by the system, while low resolution indicates more valid data after pileup rejection. Through testing, the peak counting rate reaches 12843cps, with a resolution of 6.68%, marking a significant improvement over the trapezoidal pulse forming algorithm. The system demonstrates satisfactory performance and operational effectiveness, aligning with the design objectives and presenting innovative and practical applications.