To accurately measure the uncertainty of formaldehyde emission，factors affecting the uncertainty of formaldehyde emission measurement from heavy-duty methanol engines are analyzed from various aspects，such as man，machine，material，method，and environment. A mathematical model of formaldehyde emission is established，and the relative standard uncertainty of formaldehyde emission is calculated using the world harmonized transient cycle（WHTC）test bench. The results show that the uncertainty of formaldehyde emission is related to the repeatability of measurement，the relative standard uncertainty of formaldehyde mass concentration dilution factor，total volume after exhaust dilution，and the relative standard uncertainty of actual cycle work. Among them，the dilution factor had a greater impact. The average formalhyde emission of the cold WHTC test is 41.6 mg/（kW·h），and the standard uncertainty of formaldehyde emission measurement is 1.29 mg/（kW·h），with an expanded uncertainty of 2.58 mg/（kW·h）. This research can provide a technical reference improving the accuracy and reproducibility of emission measurement of unconventional pollutants such as methanol and formaldehyde.