To clear the differences of alkaloid content and composition in natural Sophora moorcroftiana seeds among groups and within the group, the study chose S. moorcroftiana seeds from 10 groups lived at altitudes ranging from 2 900 meters to 4 100 meters in Tibet “one river and four streams” basin, adopted high performance liquid chromatography to measure important alkaloid content including oxymatrine, matrine, sophocarpine and sophoridine in 300 single plant seeds from 10 groups, used software SPSS for variance analysis, correlation analysis and cluster analysis, analyzed the relationship between geographic distribution and alkaloid content as well as heredity and variation among groups and screened out groups with higher alkaloid to provide S. moorcroftiana medicine exploitation and utilization with evidence. The result showed that: (1) oxymatrine, matrine and sophocarpine were all detected in S. moorcroftiana seeds of 10 groups and their contents were oxymatrine (46.18-64.08 mg/g)>matrine (1.14-9.82 mg/g)> sophocarpine (0.08-1.16 mg/g) in descending order, where oxymatrine content accounted for over 90% of total alkaloid, highest in group 4 (64.08±7.37 mg/g); others were little alkaloid, highest in group 3. There were significant differences of oxymatrine, matrine and sophocarpine among groups (P ＜0.01). (2) Oxymatrine had relevant less variation within the group and among groups; matrine and sophocarpine had relevant more variation within the group and among groups; moreover oxymatrine and sophocarpine had relevant more variation among groups than within the group; matrine had relevant less variation among groups than within the group. (3) Oxymatrine had significant positive correlation with altitude(r = 0.117^*). Matrine had extremely significant negative correlation with altitude, longitude and latitude (r ＜ -0.326^**). Others did not have obvious relationship. Oxymatrine had significant negative correlation with matrine as well as sophocarpine (r ＜ -0.162^**), while matrine had significant positive correlation with sophocarpine (r =0.789^**). (4) We could clarify 10 groups into 4 categories through cluster analysis. There were great differences among categories and most of differences were related to geography.