Abstract: In response to the demand for ultra-high cleanliness (ISO Class 10) and batch calibration of thousand-level vacuum gauges for the superconducting acceleration cavity of the Shenzhen high-frequency X-ray free electron laser device (S3FEL), this paper developed a multi-channel synchronous comparison calibration device in an ultra-clean environment. By integrating dynamic flow balance control, a micrometer particle control system, and a magnetic field compensation design, the three major technical challenges associated with traditional calibration equipment-insufficient cleanliness, low calibration efficiency, and cold cathode gauge tube magnetic field interference have been solved. Based on molecular flow field theory and Monte Carlo simulation optimization of the calibration chamber structure, combined with 316L stainless steel expansion chamber, an axisymmetric pressure distribution was achieved with a pressure gradient Δp/p₀ ≤ 7%. Experiments have shown that the maximum vacuum of the system reaches 4.5×10⁻⁸ Pa, which is consistent with the simulation results of 4.5×10⁻⁸ Pa. The dynamic flow control accuracy is better than ± 1×10⁻¹⁰ Pa·m³·s⁻¹, and the calibration range covers 10⁻⁴ ~10⁻⁸ Pa. Using the device, comparison experiments of cold cathode gauges were performed, showing indication deviations between −38.7% and +41.5% over the 10⁻⁸ to 10⁻⁴ Pa range, consistent with typical metrological characteristics of such gauges. The single calibration efficiency is greatly improved, meeting the regulatory calibration requirements of the S3FEL ultra-clean vacuum system. This study provides a high confidence solution for the vacuum metrology system of large scientific devices.