The study of intra-seasonal variation of sea surface chlorophyll a in the South China Sea (SCS) is helpful to promote the understanding of regional oceanic characteristics and the forecasting of fish activity information. Based on satellite data, this study analyzes the intra-seasonal variation in different seasons in the SCS, and finds that the magnitude of intra-seasonal variation of sea surface chlorophyll a is the highest in winter. In winter and spring, the regions with strong intra-seasonal variation are located to the northwest of the Luzon Island. In summer and fall, the regions with strong variation are shifted to the vicinity of the Philippine Islands. Correlation analysis shows that there is a tight relation between the intra-seasonal variation of sea surface temperature and the sea surface chlorophyll a, which is negative, and more significant in winter than in summer. In most regions, the correlation between the intra-seasonal variation of sea surface height and the sea surface chlorophyll a is not significant, but in the south-eastern rim of the SCS basin the correlation is positive. The above-mentioned features are likely caused by the anticlockwise basin scale circulation in winter. Analysis also shows that, except for the south-eastern rim of the SCS, the area to the south-east of the Hainan Island, and that to the west of the Luzon Island, magnitude of wind stress and sea surface heat flux are positively correlated with the sea surface chlorophyll a intra-seasonal time scale. Our study indicates that non-local factors and ocean dynamical adjustments might play an important role in the intra-seasonal variation of sea surface chlorophyll a in the region to the west of Luzon Island and in the south-eastern rim of the SCS basin.