Functional-structural plant models (FSPMs) generally simulate plant development and growth at the level of individual organs (leaves, flowers, internodes, etc.). Parameters that are not directly measurable, such as the sink strength of organs, can be estimated inversely by fitting the weights of organs along an axis (organic series) with the corresponding model output. To accommodate intracanopy variability among individual plants, stochastic FSPMs have been built by introducing the randomness in plant development; this presents a challenge in comparing model output and experimental data in parameter estimation since the plant axis contains individual organs with different amounts and weights. To achieve model calibration, the interaction between plant development and growth is disentangled by first computing the occurrence probabilities of each potential site of phytomer, as defined in the developmental model (potential structure). On this basis, the mean organic series is computed analytically to fit the organ-level target data. This process is applied for plants with continuous and rhythmic development simulated with different development parameter sets. The results are verified by Monte-Carlo simulation. Calibration tests are performed both in silico and on real plants. The analytical organic series are obtained for both continuous and rhythmic cases, and they match well with the results from Monte-Carlo simulation, and vice versa. This fitting process works well for both the simulated and real data sets; thus, the proposed method can solve the source-sink functions of stochastic plant architectures through a simplified approach to plant sampling. This work presents a generic method for estimating the sink parameters of a stochastic FSPM using statistical organ-level data, and it provides a method for sampling stems. The current work breaks a bottleneck in the application of FSPMs to real plants, creating the opportunity for broad applications.