The soybean is one of main sources of plant protein and fat for human diet. Increasing protein and fat contents has become an important breeding target in soybean breeding program. In this study, protein and fat contents of 77 soybean mini core gerrmplasm were analyzed using NIR technique. Genetic variation and of protein and fat content and their relationship with main agronomic traits were evaluated. The results were as follows: There was significant difference in protein and fat contents among varieties and ecological regions, which explained the abundant genetic variation of protein and fat contents in the soybean germplasm; protein content ranged from 40.68% to 50.03%, with the mean 45.95%, coefficient of variation was 4.42%; fat content ranged from 13.81% to 21.51%, with the mean 17.42%, coefficient of variation was 7.96%. Protein content showed different trend in varieties from different ecological area, southern varieties＞varieties from Huanghuaihai area＞Northern varieties＞Foreign varieties, black＞brown＞yellow＞green, and it was reverse for fat content. The protein content was negatively correlated with fat content, No. of grains per plant and No. of effective pods per plant (r=-0.825**, r=-0.205**, r=-0.156*); protein content was positively correlated with height of the lowest pod (r=0.240**).