Pollution index is a powerful tool for ecological geochemistry assessment. The commonly used pollution indices by heavy metals in soils and sediments were classified as two types of single index and integrated index in an algorithm point of view. Four single indices of contamination factor (or concentration factor), ecological risk factor, enrichment factor, and index of geo-accumulation were illustrated, and the reference values for calculating single indices were distinguished into background levels and threshold pollution values. Eight integrated indices were divided into two groups. One group is suitable for the normal distribution single indices including the sum, average, weighted average,vector modulus, and Nemerow pollution indices, and the other for log-normal distribution including the product, root of product, and weighted power product pollution indices. Using background levels as reference values, five contamination classes were divided, and the terminologies are suggested for the single and integrated indices to unify the assessment results. Software of EGAPI was developed in a single document interface to calculate the four single and eight integrated indices by heavy metals to assess the quality of soil and sediment ecological geochemistry. Pollution indices by heavy metals of Cu,Pb, and Zn in soils in parks of Beijing were calculated using EGAPI software, and these five contamination classes and terminologies suggested in this study were evaluated and used. Results ofintegrated indices of Cu, Pb, and Zn in soils indicated that the soil qualities are unpolluted as a whole and varied from low polluted to unpolluted status from the center to the outskirts of Beijing City.