We present a numerical algorithm for a stochastic age-dependent cooperative Lotka–Volterra system that incorporates a partially truncated function. Since it is challenging to obtain the real solution for this system, and traditional numerical algorithms often experience blow-up phenomena, we design a partially truncated algorithm to ensure the solution remains well behaved. We further establish the convergence of the algorithm and obtain its convergence order. Finally, numerical simulations are presented to demonstrate our theoretical findings.