Currently, it is still a challenge to study the degradation mechanisms of the space traveling wave tube amplifier (TWTA) with no failure and small sample tests. Given that the Copula functions are used to describe the correlation of multiple performance characteristics, this paper develops a bivariate hybrid stochastic degradation model to evaluate the in-orbit reliability of TWTA. Firstly, based on the impact analysis of the life of TWTA, helix current and anode voltage are selected as the performance degradation parameters. Secondly, stochastic processes with random effects based on the one-dimensional Wiener process and Gamma process are applied to describe the degradation of TWTA’s helix current and anode voltage, respectively, and the corresponding marginal distribution function is obtained. Then, the Copula function is utilized to describe the correlation between two different performance parameters of TWTA. Meanwhile, this paper also proposed a two-step method to estimate the reliability level of TWTA based on its in-orbit telemetry data through a two-step method, which contains a Markov Chain Monte Carlo (MCMC) algorithm and a maximum likelihood estimation (MLE) algorithm. Besides, the Bayes-Bootstrap sampling method is also used to improve the evaluation accuracy to overcome the defect of an in-orbit small sample of TWTA. Finally, a TWTA degradation case with a set of telemetry data is carried out, and the results show that the method proposed in this paper is more applicable and more accurate than other methods.