Saline-alkaline stress is a critical limiting factor for high-yield and stable production of rice. Elucidating the effects of different Saline-alkali soils on rice panicle morphology, and screening saline-alkali-tolerant rice germplasm accessions are of great significance to the breeding of saline-alkali tolerant rice varieties. In the present study, normal paddy soil was used as control (CK), with two different types of saline-alkali soil being used as experimental treatments. Treatment I focused on salt stress, while treatment II focused on alkali stress. A total of 164 japonica rice germplasm were examined for 11 panicle traits. Then, multivariate statistical methods, such as correlation analysis, principal component analysis (PCA), linear regression analysis (LRA) and path analysis were used to comprehensively evaluated the panicle traits of these japonica rice germplasm under different saline and alkaline adversities. The results indicated that under the two saline-alkali treatments, spike length (SL), grain number per panicle (GNP), grain density (GD), grain number of primary branch (GNPB), primary branch number (PBN), grain number of secondary branch (GNSB), and secondary branch number (SBN), were significantly reduced compared to CK. Compared with treatment II, Treatment I showed significantly increased in SL, GNP, secondary branch grain density (SBGD), GNSB, and SBN. Under different treatment conditions, variations in the correlation among 11 panicle traits were noted. Particularly, there was a significant positive correlation (p<0.01) between the thousand grain weight (TGW) and seed setting rate (SSR) under the two saline-alkali conditions, while there was no significant correlation under CK condition. PCA with 11 evaluation index from CK, treatment I and treatment II suggested three major components, with cumulative contribution rate of 80.4%, 86.4% and 83.9%, respectively. Using LRA and PCA, GNP, GD, GNPB and PBN were selected as the key indexes for evaluating panicle morphology of japonica rice under saline-alkali condition. Five saline-alkali-tolerant japonica rice accessions, namely Liaogeng 1201, Pinggeng 8, Fengdao 508, Song 820, and Ninghui 1, identified through a comprehensive evaluation value D of panicle traits can be used as valuable assets for rice-plant-architecture breeding under intricate saline-alkali environments.