In this study, we focused on two plant species in the genus Salsola (Chenopodiaceae), Salsola affinis C. A. Mey. and Salsola nitraria Pall., which are distributed in the Junggar Basin, Sinkiang, northwest China. We compared the characteristic of within-population reproductive allocation of different-sized plants (large, medium, and small) of S. affinis and S. nitraria at different altitudes using the ratios (the percentage of total biomass in reproductive biomass). In addition, we analyzed the relationship between reproductive biomass (R) and vegetative biomass (V) and the size-dependent allocation at different altitudes using a classical allometric model. We obtained the following results. (1) There were different levels of allometry between the R and V at different altitudes. The allometric slope (exponent) of the R-V relationship increased significantly with increasing altitude for S. affinis; however, there was a significant negative relationship for S. nitraria. We also found a significant positive relationship between the intercept of the regression of log R on log V and elevation for S. nitraria, although the relationship was not significant among populations of S. affinis. (2) There was a negative correlation at lower altitude and a positive correlation at higher altitude for the relationship between individual size and reproductive allocation in S. affinis. Conversely, there was a positive correlation at lower altitude and a negative correlation at higher altitude for the relationship between individual size and reproductive allocation in S. nitraria. This indicates that these Salsola species exhibit contrasting adaptation strategies. (3) Plants within the same population of S. affinis and S. nitraria were divided into three size classes, large, medium, and small. Multiple comparisons showed that, at lower altitudes, the reproductive allocation of small and medium-sized individuals of S. affinis was significantly higher than that of large individuals, but that at higher altitudes, the reproductive allocation of large individuals was significantly higher. In contrast, the reproductive allocation of large individuals of S. nitraria was significantly higher than that of medium-sized and small individuals at lower altitudes, whereas the reproductive allocation of small individuals was significantly higher than that of medium-sized and large individuals at higher altitudes. Comprehensive analysis suggests that two Salsola species adopt different reproductive allocation strategies concomitant with a change in elevation. In addition to the genetic effect, the environment and individual size had significant influences on the variation in reproductive allocation of S. nitraria, whereas individual size in S. affinis had no significant influence on the variation in reproductive allocation with altitude. The microenvironment of the arid Junggar Basin region also had an impact on individual plant size in the same population, and produced different reproductive allocation patterns. We therefore suggest that more attention should be paid to the impact of individual size on reproductive allocation in arid areas.