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The rare earth elements and yttrium (REY)-enriched phosphorites in the Zhijin region, southwest China, have attracted much attention, yet its origin has not been sufficiently addressed. The geology, mineralogy and geochemistry of samples from four sections of the early Cambrian age from the Zhijin region were studied to attain the redox condition and origin of REY. Data from in situ analysis show that REY are mainly contained in francolite, and the two types of francolite (bioclastic and granular) have no distinct difference in REY content (ΣREY). A Ce anomaly indicates an oxic condition in primary seawater. An Eu anomaly and ratios of redox sensitive elements (RSEs) indicate a fluctuating redox condition during phosphorite deposition. Shale-normalized REY patterns of whole rock and francolite show a hat-shaped pattern, indicating the effect of diagenetic processes. The Y/Ho ratio of the selected sections ranges from 38.13 to 61.93, and together with the Y anomaly, La_N/Nd_N ratio, La_N/Sm_N ratio, and La_N/Yb_N ratio, this indicates a seawater origin. This is supported by the Ce/Ce* of the phosphorite that ranges from 0.32 to 0.52 and the Eu/Eu* that ranges from 0.88 to 1.82, which is similar to the characteristics of seawater and deep-sea mud. We also propose a minor contribution of terrigenous debris and influence of diagenesis and hydrothermal processes.