The Water Cherenkov detector array (WCDA), one of major parts of LHAASO project, has been partly operated since April 2019. There are two types of PMT hung in center of each cell of WCDA. In order to achieve an optimal energy reconstruction, and cosmic ray background suppression, we develop an off-line method to calibrate number of photoelectrons of signals. By matching signals caught by different kinds of PMT, we bridge their linear measurement range to obtain equivalent NPE of signals up to more than $8\times10^6$ PEs for WCDA-1, and more than $1.5\times10^5$ PEs for WCDA-2. Besides, detector monitoring and various measurements show the PMT among cells are slightly different in quantum efficiency and collection efficiency, and the light attenuation and depth of water in the pool are also varying with time, especially in the very beginning of the operation. Above inhomogeneity and instablibility influence the detection efficiency of cells on secondary air shower particles. Based on previous research, the single particle peak in the charge spectrum of single cell mainly formed by muon signals are used to calibrate the detection efficiency difference as well as long term variation of all the detector cells. A possibly more flexible efficiency calibration method of Constant Rate Scaling is also under study. The analysis method and the calibration results of the first two pools are presented in this paper.