The invention provides a GNSS satellite clock error real-time estimation quality control method aimed at characteristics that real-time clock error estimation has high requirement on observation data quality and cannot perform post residual error edition. The method comprises two aspects: first step, before parameter estimation, preprocessing original observation data, including gross error rejecting and cycle slip detection; second step, after update of filter observation, based on a posttest observed value residual error, analyzing and processing a gross error and cycle slip which are not detected in a previous step, specifically including steps of establishing a square root information filtering algorithm model, processing noise; smoothing square root information; and based on square root information filtering, performing real-time quality control. The method can realize preprocessing of real-time clock error data and efficient quality control, and can efficiently find out problematic observed quantity, prevents filter divergence, so as to realize real-time clock error stable estimation and satisfy real-time high-precision positioning requirement.