Improved Geometrical Product Specifications (GPS) is an internationally accepted standards system. It is the foundation of the technology standards and metrology specifications. Uncertainty is one of the most important concepts in improved GPS. In the improved GPS standards system, uncertainty is used as an economic tool to enable optimum allocation of resources amongst specification, manufacturing and verification. Estimation of uncertainty in measurement according to improved GPS can improve the reliability of the measurement. A method to estimate the uncertainty in straightness measurement is proposed according to the requirements of improved GPS standard system. Based on the mini-zone method and the transparent box model, the calculation equation of uncertainty in straightness measurement is deduced. The experiment indicates that this method may assure the integrity of the verification result and improve the reliability of measurement.