Elliptical micro-pit array was fabricated on the plane section of boron cast iron cylinder liner with nanosecond pulse laser. The influence of filling processing method and parameters on surface morphology of elliptical micro-pits was studied. The results show that the ring filling has better surface morphology than other three processing methods. The maximum depth and the maximum area of the micro-pit length-diameter section increased as the filling line width decreased, and the maximum depth reached 218 μm. When the filling line width is greater than or equal to 3 μm, the molten material at the bottom of the micro pit decreases obviously. The influence of scanning speed on the morphology of micro-pits was related to the filling line width. When the filling line width was small, maximum depth and the maximum area tended to increase and then decrease with scanning speed increased, the inflection point is 400 mm/s. When the filling line width was large, maximum depth and the maximum area were inversely proportional to scanning speed. Laser frequency has limited influence on maximum depth and the maximum area. The maximum area change rate is only 5.61%, which mainly shows that the bottom of the micro pit tends to be more gentle with the increase of frequency.