Pipeline filter algorithm proposes a solution of detection of dim small target from the perspective of time domain. In terms of detection of weak point target in the strongly undulant infrared sky background, a pipeline filter algorithm is proposed based on motion direction estimation as a method to improve the flaw of detection probability deduction due to the strong interferential noise within the pipeline and low signal noise ratio. The motion characteristics of infrared weak point target are analyzed and the motion direction estimation model was established according to the continuity characteristic of the targets between consecutive frames. Through the model, the prior position information of the targets is detected frame by frame and analyzed in order to estimate the motion direction and trajectory of the targets. The estimation results are used to eliminate the interference on the targets caused by the pipeline inner noises. Experiments and simulation results show that the algorithm can suppress noises in the pipeline effectively, increase the detection probability of the targets, and strengthen the resistance characteristic of the targets against the noises within the pipe.