The Large High Altitude Air Shower Observatory (LHAASO) is a multi-purpose experiment, which is now under construction at Mt. Haizishan (4410 m a.s.l.), Daocheng, Sichun, China. The 78,000 m$^2$ Water Cherenkov Detector Array (WCDA), one of main components of the LHAASO, can be able to survey the gamma-ray sky continuously in a wide energy range. The precision of the angular resolution is a key factor for the detection sensitivity of the gamma-ray sources. To reach the designed angular resolution, a time calibration system with a good accuracy is needed. A hardware calibration system based on optical fibers and blue LEDs have be deployed in WCDA, which provides initial time offsets for later analysis. Beside some other factors, such as PMT position differences and other unknown effects, will introduce additional time offsets between the detector cells. In order to calibrate such differences, an offline software calibration procedure based on the offline air shower data is suggested. In this paper, all above details in hardware and offline software calibration are introduced, some preliminary experimental result are also presented.